Mock Version: 3.0 Mock Version: 3.0 Mock Version: 3.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target aarch64 --nodeps /builddir/build/SPECS/apbs.spec'], chrootPath='/var/lib/mock/f37-build-36895114-4719645/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target aarch64 --nodeps /builddir/build/SPECS/apbs.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1658275200 Wrote: /builddir/build/SRPMS/apbs-3.0.0-16.fc37.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target aarch64 --nodeps /builddir/build/SPECS/apbs.spec'], chrootPath='/var/lib/mock/f37-build-36895114-4719645/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target aarch64 --nodeps /builddir/build/SPECS/apbs.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1658275200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jpso89 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf apbs-3.0.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/apbs-3.0.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd apbs-3.0.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (apbs-cmake.patch):' Patch #0 (apbs-cmake.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p2 -b --suffix .apbs-cmake --fuzz=0 patching file CMakeLists.txt patching file src/CMakeLists.txt patching file tools/manip/CMakeLists.txt patching file tools/mesh/CMakeLists.txt Patch #1 (apbs-exclude_tests.patch): + echo 'Patch #1 (apbs-exclude_tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .exclude_tests --fuzz=0 patching file tests/test_cases.cfg Patch #2 (apbs-python311.patch): + echo 'Patch #2 (apbs-python311.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .python311 --fuzz=0 patching file tools/manip/inputgen.py + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING + cp -p /builddir/build/SOURCES/apbs-LGPL_V2 contrib/iapbs/iapbs-LGPLv2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.QisrPZ + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/apbs-3.0.0/.package_note-apbs-3.0.0-16.fc37.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh apbs 3.0.0-16.fc37 aarch64 + cd apbs-3.0.0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + export 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + mkdir -p build + cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF -DENABLE_FETK:BOOL=OFF '-DCMAKE_C_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG' '-DCMAKE_CXX_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG' -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSHARE_INSTALL_PREFIX:PATH=/usr/share CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0054 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- The C compiler identification is GNU 12.1.1 -- The CXX compiler identification is GNU 12.1.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Inline functions enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_routines -- External Headers: -- -- APBS Libraries: m;stdc++;maloc;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines -- -- -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -- Building documentation enabled -- Found Doxygen: /usr/bin/doxygen (found version "1.9.4") found components: doxygen dot -- Supplemental tools enabled -- Building mesh -- libraries: apbs -- Building manip -- libraries: apbs CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.0.2") -- Found Python3: /usr/bin/python3.11 (found version "3.11.0") found components: Interpreter Development Development.Module Development.Embed -- ******* Python3 FOUND -- ***** Python3 include path is: /usr/include/python3.11 -- ***** Python3 library path is: /usr/lib64/libpython3.11.so -- ***** Python3 library dir is: /usr/lib64 -- Building of iAPBS interface enabled -- Found Python3: /usr/bin/python3.11 (found version "3.11.0") found components: Interpreter -- ******* Python3 FOUND /usr/bin/python3.11 -- TEST born_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t born -- TEST actin-dimer-auto_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-auto -- TEST actin-dimer-parallel_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-parallel -- TEST alkanes_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t alkanes -- TEST FKBP_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t FKBP -- TEST hca-bind_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t hca-bind -- TEST ionize_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ionize -- TEST ion-pmf_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-pmf -- TEST ion-protein_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-protein -- TEST pka-lig_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t pka-lig -- TEST point-pmf_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t point-pmf -- TEST solv_test COMMAND /usr/bin/python3.11 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t solv -- Configuring done -- Generating done -- Build files have been written to: /builddir/build/BUILD/apbs-3.0.0/build + make -O -j1 V=1 -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[1]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 1%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:816:13: warning: variable 'isBinary' set but not used [-Wunused-but-set-variable] 816 | int isBinary = 0; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:813:25: warning: unused variable 'itmp' [-Wunused-variable] 813 | size_t i, j, k, itmp, u; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_writeUHBD': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:36: warning: variable 'hy' set but not used [-Wunused-but-set-variable] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:30: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:853:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 2%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c: In function 'Vmgrid_addGrid': /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:198:12: warning: unused variable 'tgrad' [-Wunused-variable] 198 | double tgrad[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:15: warning: unused variable 'rc' [-Wunused-variable] 197 | int i, j, rc; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:12: warning: unused variable 'j' [-Wunused-variable] 197 | int i, j, rc; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:9: warning: unused variable 'i' [-Wunused-variable] 197 | int i, j, rc; | ^ [ 3%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c: In function 'Vopot_curvature': /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:26: warning: variable 'eps_w' set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:18: warning: variable 'charge' set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:15: warning: variable 'T' set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:269:23: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 269 | u = u + val; | ~~^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:53: note: 'val' was declared here 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~ [ 4%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:157:61: warning: variable 'zkappa2' set but not used [-Wunused-but-set-variable] 157 | double ionConc[MAXION], ionQ[MAXION], ionRadii[MAXION], zkappa2, zks2; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qmEnergySMPBE': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1503:12: warning: variable 'zks2' set but not used [-Wunused-but-set-variable] 1503 | zks2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qfEnergyPoint': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1712:13: warning: variable 'pvec' set but not used [-Wunused-but-set-variable] 1712 | double *pvec; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:24: warning: variable 'zmax' set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:18: warning: variable 'ymax' set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qfAtomEnergy': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:36: warning: variable 'zmax' set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:24: warning: variable 'ymax' set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'focusFillBound': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1953:12: warning: variable 'charge' set but not used [-Wunused-but-set-variable] 1953 | charge, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1952:13: warning: variable 'apos' set but not used [-Wunused-but-set-variable] 1952 | *apos, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1951:12: warning: variable 'size' set but not used [-Wunused-but-set-variable] 1951 | size, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1950:12: warning: variable 'xkappa' set but not used [-Wunused-but-set-variable] 1950 | xkappa, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:40: warning: variable 'qzy' set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:36: warning: variable 'qzx' set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:24: warning: variable 'qyx' set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcCalcOrig': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:34: warning: unused variable 'debye' [-Wunused-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:22: warning: variable 'quadrupole' set but not used [-Wunused-but-set-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:13: warning: variable 'dipole' set but not used [-Wunused-but-set-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcflnew': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3415:31: warning: variable 'eps_p' set but not used [-Wunused-but-set-variable] 3415 | double dist, pre1, eps_w, eps_p, T, xkappa; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:29: warning: unused variable 'z1' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:25: warning: unused variable 'z0' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:21: warning: unused variable 'y1' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:17: warning: unused variable 'y0' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:13: warning: unused variable 'x1' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:9: warning: unused variable 'x0' [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:13: warning: unused variable 'k' [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:11: warning: unused variable 'j' [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:9: warning: unused variable 'i' [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'multipolebc': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3492:19: warning: variable 'kr3' set but not used [-Wunused-but-set-variable] 3492 | double kr,kr2,kr3; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_sdh': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:40: warning: variable 'qzy' set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:36: warning: variable 'qzx' set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:24: warning: variable 'qyx' set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:22: warning: unused variable 'quadrupole' [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:13: warning: unused variable 'dipole' [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_mdh': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3875:41: warning: variable 'eps_p' set but not used [-Wunused-but-set-variable] 3875 | double size, charge, xkappa, eps_w, eps_p, T, pre1, dist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:22: warning: unused variable 'quadrupole' [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:13: warning: unused variable 'dipole' [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_mem': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4008:24: warning: unused variable 'edge_L' [-Wunused-variable] 4008 | double A, B, C, D, edge_L, l; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:38: warning: unused variable 'z_shift' [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:12: warning: unused variable 'dist' [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_map': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:38: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:34: warning: variable 'hy' set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:30: warning: variable 'hx' set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4176:11: warning: unused variable 'pbe' [-Wunused-variable] 4176 | Vpbe *pbe; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMap': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4492:46: warning: unused variable 'pot' [-Wunused-variable] 4492 | double ionstr, position[3], tkappa, eps, pot, hx, hy, hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMolIon': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4638:16: warning: variable 'surfMeth' set but not used [-Wunused-but-set-variable] 4638 | Vsurf_Meth surfMeth; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4630:11: warning: variable 'acc' set but not used [-Wunused-but-set-variable] 4630 | Vacc *acc; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMolDielNoSmooth': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4746:30: warning: unused variable 'deps' [-Wunused-variable] 4746 | double srad, epsw, epsp, deps, area; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5031:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] 5031 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin, w3i; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCharge': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5289:15: warning: unused variable 'rc' [-Wunused-variable] 5289 | Vrc_Codes rc; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoChargeMap': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:49: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:45: warning: variable 'hy' set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:41: warning: variable 'hx' set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_force': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5829:12: warning: unused variable 'npF' [-Wunused-variable] 5829 | double npF[3]; /* Non-polar boundary force */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_ibForce': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5848:13: warning: variable 'alist' set but not used [-Wunused-but-set-variable] 5848 | Valist *alist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_dbForce': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:55: warning: variable 'kT' set but not used [-Wunused-but-set-variable] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:18: warning: variable 'dx' set but not used [-Wunused-but-set-variable] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:66: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'qfForceSpline2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'qfForceSpline4': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:15: warning: unused variable 'k' [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:12: warning: unused variable 'j' [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'markFrac': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6692:39: warning: variable 'a000' set but not used [-Wunused-but-set-variable] 6692 | double dx, dx2, dy, dy2, dz, dz2, a000, a001, a010, a100, r2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'zlapSolve': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6912:12: warning: unused variable 'norm' [-Wunused-variable] 6912 | double norm, coef, proj, eigx, eigy, eigz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_solveLaplace': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:35: warning: variable 'n' set but not used [-Wunused-but-set-variable] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:18: warning: unused variable 'ijk' [-Wunused-variable] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoPermanentMultipole': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:58: warning: unused variable 'mqzz' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:53: warning: unused variable 'mqzy' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:48: warning: unused variable 'mqzx' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:43: warning: unused variable 'mqyy' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:38: warning: unused variable 'mqyx' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:33: warning: unused variable 'mqxx' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:29: warning: unused variable 'muz' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:25: warning: unused variable 'muy' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:21: warning: unused variable 'mux' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:18: warning: unused variable 'mc' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:12: warning: unused variable 'debye' [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:24: warning: unused variable 'mr2' [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:20: warning: unused variable 'mkr' [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:16: warning: unused variable 'mjr' [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:12: warning: unused variable 'mir' [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7258:9: warning: unused variable 'i' [-Wunused-variable] 7258 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7253:47: warning: unused variable 'qave' [-Wunused-variable] 7253 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:29: warning: unused variable 'quad' [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:21: warning: unused variable 'dipole' [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline4': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9948:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] 9948 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9946:42: warning: unused variable 'w2i' [-Wunused-variable] 9946 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoPermanentInduced': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10278:9: warning: unused variable 'i' [-Wunused-variable] 10278 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10273:47: warning: unused variable 'qave' [-Wunused-variable] 10273 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:29: warning: unused variable 'quad' [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:21: warning: unused variable 'dipole' [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline3': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10441:27: warning: variable 'e5' set but not used [-Wunused-but-set-variable] 10441 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10439:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] 10439 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10437:42: warning: unused variable 'w2i' [-Wunused-variable] 10437 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:55: warning: variable 'mxlv' set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:47: warning: unused variable 'maxlev' [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:39: warning: unused variable 'ierror' [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:15: warning: variable 'niwk' set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:9: warning: variable 'nrwk' set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:29: warning: unused variable 'i' [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:21: warning: unused variable 'nnzero' [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:15: warning: unused variable 'ncol' [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:9: warning: unused variable 'nrow' [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:73: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10804:5: note: in expansion of macro 'MAT2' 10804 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp3': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10836:5: note: in expansion of macro 'MAT2' 10836 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp4': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10874:5: note: in expansion of macro 'MAT3' 10874 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10873:5: note: in expansion of macro 'MAT3' 10873 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10872:5: note: in expansion of macro 'MAT3' 10872 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10871:5: note: in expansion of macro 'MAT3' 10871 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10870:5: note: in expansion of macro 'MAT3' 10870 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10866:27: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 10866 | int inonz, iirow, nn, nrow, ncol, nonz, irow, n; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7229:16: warning: 'd3bspline4' defined but not used [-Wunused-function] 7229 | VPUBLIC double d3bspline4(double x) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684:15: warning: 'markFrac' defined but not used [-Wunused-function] 6684 | VPRIVATE void markFrac( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868:15: warning: 'bcfl_mdh' defined but not used [-Wunused-function] 3868 | VPRIVATE void bcfl_mdh(Vpmg *thee){ | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828:15: warning: 'bcCalcOrig' defined but not used [-Wunused-function] 2828 | VPRIVATE void bcCalcOrig(Vpmg *thee) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2547:17: warning: 'bcfl1sp' defined but not used [-Wunused-function] 2547 | VPRIVATE double bcfl1sp(double size, double *apos, double charge, | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1148:17: warning: 'Vpmg_polarizEnergy' defined but not used [-Wunused-function] 1148 | VPRIVATE double Vpmg_polarizEnergy(Vpmg *thee, | ^~~~~~~~~~~~~~~~~~ [ 5%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c: In function 'Vpmgp_size': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:204:87: warning: unused variable 'iretot' [-Wunused-variable] 204 | int nxf, nyf, nzf, level, num_nf_oper, num_narrc_oper, n_band, nc_band, num_band, iretot; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 5%] Built target apbs_mg make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 6%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function 'NOsh_setupCalcGEOFLOWMANUAL': /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2683:15: warning: variable 'apolparm' set but not used [-Wunused-but-set-variable] 2683 | APOLparm *apolparm = VNULL; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function 'NOsh_parsePBAM': /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3139:17: warning: 'strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 3139 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite -1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function 'NOsh_parsePBSAM': /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3268:17: warning: 'strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 3268 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite - 1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function 'NOsh_parseInput': /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1348:13: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1348 | strncpy(thee->apolname[thee->napol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1222:13: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1222 | strncpy(thee->elecname[thee->nelec], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:953:9: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 953 | strncpy(thee->meshpath[thee->nmesh], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:918:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 918 | strncpy(thee->chargepath[thee->ncharge], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:872:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 872 | strncpy(thee->potpath[thee->npot], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:827:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 827 | strncpy(thee->kappapath[thee->nkappa], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:772:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 772 | strncpy(thee->dielXpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:776:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 776 | strncpy(thee->dielYpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:780:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 780 | strncpy(thee->dielZpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:723:13: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 723 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:701:13: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 701 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:659:9: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 659 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:640:9: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 640 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:621:9: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 621 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ [ 8%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 9%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 10%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseRandorient': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:305:17: warning: unused variable 'name' [-Wunused-variable] 305 | const char* name = "randorient"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parse3Dmap': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:373:10: warning: unused variable 'tok' [-Wunused-variable] 373 | char tok[VMAX_BUFSIZE]; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:372:17: warning: unused variable 'name' [-Wunused-variable] 372 | const char* name = "3dmap"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseRunType': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:282:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 282 | strncpy(thee->runtype, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseRunName': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:297:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 297 | strncpy(thee->runname, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseUnits': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:344:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 344 | strncpy(thee->units, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseTermcombine': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:452:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 452 | strncpy(thee->termcombine, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseGrid2D': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:400:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 400 | strncpy(thee->grid2Dname[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:408:7: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 408 | strncpy(thee->grid2Dax[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseXYZ': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:656:8: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 656 | strncpy(thee->xyzfil[mol][thee->xyzct[mol]], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseDiff': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:500:8: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 500 | strncpy(thee->moveType[molind], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseTerm': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:563:12: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 563 | strncpy(thee->termnam[thee->termct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:573:11: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 573 | strncpy(thee->confil[thee->confilct], tok, CHR_MAXLEN); | ^ [ 11%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_parseMSMS': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:183:13: warning: unused variable 'td' [-Wunused-variable] 183 | int td; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_parseSurf': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:174:8: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 174 | strncpy(thee->surffil[thee->surfct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_parseImat': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:211:8: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 211 | strncpy(thee->imatfil[thee->imatct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_parseExp': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:226:8: warning: 'strncpy' output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 226 | strncpy(thee->expfil[thee->expct], tok, CHR_MAXLEN); | ^ [ 12%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c: In function 'PBEparm_parseWRITE': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1163:9: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1163 | strncpy(thee->writestem[thee->numwrite], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c: In function 'PBEparm_parseWRITEMAT': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1204:5: warning: 'strncpy' output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1204 | strncpy(thee->writematstem, tok, VMAX_ARGLEN); | ^ [ 13%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_check': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:36: warning: unused variable 'nlev' [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:26: warning: unused variable 'tnlev' [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:22: warning: unused variable 'ti' [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:12: warning: unused variable 'tdime' [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:9: warning: unused variable 'i' [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_copy': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:176:9: warning: unused variable 'i' [-Wunused-variable] 176 | int i; | ^ [ 14%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c: In function 'GEOFLOWparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] 79 | int i; | ^ [ 16%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o [ 17%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'VaccSurf_dtor': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:841:11: warning: variable 'mem' set but not used [-Wunused-but-set-variable] 841 | Vmem *mem; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_splineAccGradAtomNorm3': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1104:27: warning: variable 'e5' set but not used [-Wunused-but-set-variable] 1104 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_atomdSASA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1338:12: warning: variable 'ts' set but not used [-Wunused-but-set-variable] 1338 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1335:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] 1335 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_totalAtomdSASA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1395:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] 1395 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1392:23: warning: variable 'tRad' set but not used [-Wunused-but-set-variable] 1392 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1391:9: warning: variable 'iatom' set but not used [-Wunused-but-set-variable] 1391 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_totalAtomdSAV': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1454:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] 1454 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1451:23: warning: variable 'tRad' set but not used [-Wunused-but-set-variable] 1451 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1450:9: warning: variable 'iatom' set but not used [-Wunused-but-set-variable] 1450 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_wcaEnergyAtom': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1584:9: warning: variable 'npts' set but not used [-Wunused-but-set-variable] 1584 | int npts[3]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_wcaForceAtom': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1807:12: warning: variable 'ts' set but not used [-Wunused-but-set-variable] 1807 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1764:9: warning: variable 'npts' set but not used [-Wunused-but-set-variable] 1764 | npts[3], | ^~~~ [ 18%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c: In function 'Valist_readPQR': /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:618:10: warning: unused variable 'chs' [-Wunused-variable] 618 | char chs[VMAX_BUFSIZE]; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c: In function 'Valist_readXML': /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:834:17: warning: 'radius' may be used uninitialized [-Wmaybe-uninitialized] 834 | Vatom_setRadius(nextAtom, radius); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:29: note: 'radius' was declared here 736 | double x, y, z, charge, radius, dtmp; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:833:17: warning: 'charge' may be used uninitialized [-Wmaybe-uninitialized] 833 | Vatom_setCharge(nextAtom, charge); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:21: note: 'charge' was declared here 736 | double x, y, z, charge, radius, dtmp; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:831:48: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 831 | pos[0] = x; pos[1] = y; pos[2] = z; | ~~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:18: note: 'z' was declared here 736 | double x, y, z, charge, radius, dtmp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:831:36: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] 831 | pos[0] = x; pos[1] = y; pos[2] = z; | ~~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:15: note: 'y' was declared here 736 | double x, y, z, charge, radius, dtmp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:831:24: warning: 'x' may be used uninitialized [-Wmaybe-uninitialized] 831 | pos[0] = x; pos[1] = y; pos[2] = z; | ~~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:12: note: 'x' was declared here 736 | double x, y, z, charge, radius, dtmp; | ^ [ 19%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 20%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o [ 21%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o [ 22%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o [ 24%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o [ 25%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c: In function 'Vparam_readXMLFile': /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:394:17: warning: 'nalloc' may be used uninitialized [-Wmaybe-uninitialized] 394 | Vmem_free(thee->vmem, nalloc, sizeof(Vparam_AtomData), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 395 | (void **)&(atoms)); | ~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:309:26: note: 'nalloc' was declared here 309 | int i, ires, natoms, nalloc, ralloc; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:400:27: warning: 'natoms' may be used uninitialized [-Wmaybe-uninitialized] 400 | atom = &(atoms[natoms]); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:309:18: note: 'natoms' was declared here 309 | int i, ires, natoms, nalloc, ralloc; | ^~~~~~ [ 26%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulomb_direct': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:31: warning: unused variable 'fz' [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:27: warning: unused variable 'fy' [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:23: warning: unused variable 'fx' [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:16: warning: unused variable 'qtemp' [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:13: warning: unused variable 'q' [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulomb': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:264:9: warning: unused variable 'iatom' [-Wunused-variable] 264 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:31: warning: unused variable 'fz' [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:27: warning: unused variable 'fy' [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:23: warning: unused variable 'fx' [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:16: warning: unused variable 'qtemp' [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:13: warning: unused variable 'q' [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:45: warning: unused variable 'scale' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:41: warning: unused variable 'dz' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:37: warning: unused variable 'dy' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:33: warning: unused variable 'dx' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:27: warning: unused variable 'dist' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:19: warning: unused variable 'charge' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:13: warning: unused variable 'apos' [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:261:12: warning: unused variable 'atom' [-Wunused-variable] 261 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulombD_direct': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:16: warning: unused variable 'qtemp' [-Wunused-variable] 316 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:13: warning: unused variable 'q' [-Wunused-variable] 316 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulombD': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:368:9: warning: unused variable 'iatom' [-Wunused-variable] 368 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:16: warning: unused variable 'qtemp' [-Wunused-variable] 367 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:13: warning: unused variable 'q' [-Wunused-variable] 367 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:60: warning: unused variable 'scale' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:56: warning: unused variable 'dx' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:52: warning: unused variable 'dz' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:48: warning: unused variable 'dy' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:40: warning: unused variable 'idist3' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:33: warning: unused variable 'dist2' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:27: warning: unused variable 'dist' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:19: warning: unused variable 'charge' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:13: warning: unused variable 'apos' [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:365:12: warning: unused variable 'atom' [-Wunused-variable] 365 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525:14: warning: 'treecalc' defined but not used [-Wunused-function] 525 | VPRIVATE int treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505:14: warning: 'treecleanup' defined but not used [-Wunused-function] 505 | VPRIVATE int treecleanup(Vgreen *thee) { | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425:14: warning: 'treesetup' defined but not used [-Wunused-function] 425 | VPRIVATE int treesetup(Vgreen *thee) { | ^~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 26%] Built target apbs_generic make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 27%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function 'VbuildA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:66:5: note: in expansion of macro 'MAT2' 66 | MAT2(ac, *nx * *ny * *nz, 14); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function 'VbuildA_fv': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:167:5: note: in expansion of macro 'MAT3' 167 | MAT3(gzcf, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gycf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:166:5: note: in expansion of macro 'MAT3' 166 | MAT3(gycf, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:165:5: note: in expansion of macro 'MAT3' 165 | MAT3(gxcf, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:164:5: note: in expansion of macro 'MAT3' 164 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:163:5: note: in expansion of macro 'MAT3' 163 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:162:5: note: in expansion of macro 'MAT3' 162 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:161:5: note: in expansion of macro 'MAT3' 161 | MAT3(a3cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:160:5: note: in expansion of macro 'MAT3' 160 | MAT3(a2cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:159:5: note: in expansion of macro 'MAT3' 159 | MAT3(a1cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:158:5: note: in expansion of macro 'MAT3' 158 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_ccf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:157:5: note: in expansion of macro 'MAT3' 157 | MAT3( ccf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:156:5: note: in expansion of macro 'MAT3' 156 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:155:5: note: in expansion of macro 'MAT3' 155 | MAT3( fcf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:154:5: note: in expansion of macro 'MAT3' 154 | MAT3( fc, *nx, *ny, *nz); | ^~~~ [ 28%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:65:5: note: in expansion of macro 'MAT2' 65 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband1_7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:133:5: note: in expansion of macro 'MAT3' 133 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:132:5: note: in expansion of macro 'MAT3' 132 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:131:5: note: in expansion of macro 'MAT3' 131 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:130:5: note: in expansion of macro 'MAT3' 130 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acB' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:128:5: note: in expansion of macro 'MAT2' 128 | MAT2(acB, *lda, *ny-1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband1_27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:213:5: note: in expansion of macro 'MAT3' 213 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:212:5: note: in expansion of macro 'MAT3' 212 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:211:5: note: in expansion of macro 'MAT3' 211 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:210:5: note: in expansion of macro 'MAT3' 210 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:208:5: note: in expansion of macro 'MAT3' 208 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:207:5: note: in expansion of macro 'MAT3' 207 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:206:5: note: in expansion of macro 'MAT3' 206 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:205:5: note: in expansion of macro 'MAT3' 205 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:203:5: note: in expansion of macro 'MAT3' 203 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:202:5: note: in expansion of macro 'MAT3' 202 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:200:5: note: in expansion of macro 'MAT3' 200 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:199:5: note: in expansion of macro 'MAT3' 199 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:198:5: note: in expansion of macro 'MAT3' 198 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:197:5: note: in expansion of macro 'MAT3' 197 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acB' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:195:5: note: in expansion of macro 'MAT2' 195 | MAT2(acB, *lda, *ny-1); | ^~~~ [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:64:5: note: in expansion of macro 'MAT2' 64 | MAT2( ac, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acFF' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:63:5: note: in expansion of macro 'MAT2' 63 | MAT2(acFF, *nxf * *nyf * *nzf, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pcFF' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:62:5: note: in expansion of macro 'MAT2' 62 | MAT2(pcFF, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_1': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:216:5: note: in expansion of macro 'MAT3' 216 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:215:5: note: in expansion of macro 'MAT3' 215 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:214:5: note: in expansion of macro 'MAT3' 214 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:213:5: note: in expansion of macro 'MAT3' 213 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:212:5: note: in expansion of macro 'MAT3' 212 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:211:5: note: in expansion of macro 'MAT3' 211 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:210:5: note: in expansion of macro 'MAT3' 210 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:209:5: note: in expansion of macro 'MAT3' 209 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:208:5: note: in expansion of macro 'MAT3' 208 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:206:5: note: in expansion of macro 'MAT3' 206 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:205:5: note: in expansion of macro 'MAT3' 205 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:204:5: note: in expansion of macro 'MAT3' 204 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:203:5: note: in expansion of macro 'MAT3' 203 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:202:5: note: in expansion of macro 'MAT3' 202 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:201:5: note: in expansion of macro 'MAT3' 201 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:200:5: note: in expansion of macro 'MAT3' 200 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:199:5: note: in expansion of macro 'MAT3' 199 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:198:5: note: in expansion of macro 'MAT3' 198 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:196:5: note: in expansion of macro 'MAT3' 196 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:195:5: note: in expansion of macro 'MAT3' 195 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:194:5: note: in expansion of macro 'MAT3' 194 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:193:5: note: in expansion of macro 'MAT3' 193 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:192:5: note: in expansion of macro 'MAT3' 192 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:191:5: note: in expansion of macro 'MAT3' 191 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:190:5: note: in expansion of macro 'MAT3' 190 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:189:5: note: in expansion of macro 'MAT3' 189 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:188:5: note: in expansion of macro 'MAT3' 188 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:186:5: note: in expansion of macro 'MAT3' 186 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:185:5: note: in expansion of macro 'MAT3' 185 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:184:5: note: in expansion of macro 'MAT3' 184 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:183:5: note: in expansion of macro 'MAT3' 183 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:182:5: note: in expansion of macro 'MAT3' 182 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:181:5: note: in expansion of macro 'MAT3' 181 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:180:5: note: in expansion of macro 'MAT3' 180 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:179:5: note: in expansion of macro 'MAT3' 179 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:177:5: note: in expansion of macro 'MAT3' 177 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:176:5: note: in expansion of macro 'MAT3' 176 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:174:5: note: in expansion of macro 'MAT3' 174 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:172:5: note: in expansion of macro 'MAT3' 172 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:171:5: note: in expansion of macro 'MAT3' 171 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:170:5: note: in expansion of macro 'MAT3' 170 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:168:5: note: in expansion of macro 'MAT3' 168 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:163:33: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] 163 | int iim1, iip1, jjm1, jjp1, kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:532:5: note: in expansion of macro 'MAT3' 532 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:531:5: note: in expansion of macro 'MAT3' 531 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:530:5: note: in expansion of macro 'MAT3' 530 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:529:5: note: in expansion of macro 'MAT3' 529 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:528:5: note: in expansion of macro 'MAT3' 528 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:527:5: note: in expansion of macro 'MAT3' 527 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:526:5: note: in expansion of macro 'MAT3' 526 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:525:5: note: in expansion of macro 'MAT3' 525 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:524:5: note: in expansion of macro 'MAT3' 524 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:522:5: note: in expansion of macro 'MAT3' 522 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:521:5: note: in expansion of macro 'MAT3' 521 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:520:5: note: in expansion of macro 'MAT3' 520 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:519:5: note: in expansion of macro 'MAT3' 519 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:518:5: note: in expansion of macro 'MAT3' 518 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:517:5: note: in expansion of macro 'MAT3' 517 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:516:5: note: in expansion of macro 'MAT3' 516 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:515:5: note: in expansion of macro 'MAT3' 515 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:514:5: note: in expansion of macro 'MAT3' 514 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:512:5: note: in expansion of macro 'MAT3' 512 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:511:5: note: in expansion of macro 'MAT3' 511 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:510:5: note: in expansion of macro 'MAT3' 510 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:509:5: note: in expansion of macro 'MAT3' 509 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:508:5: note: in expansion of macro 'MAT3' 508 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:507:5: note: in expansion of macro 'MAT3' 507 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:506:5: note: in expansion of macro 'MAT3' 506 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:505:5: note: in expansion of macro 'MAT3' 505 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:504:5: note: in expansion of macro 'MAT3' 504 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:502:5: note: in expansion of macro 'MAT3' 502 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:501:5: note: in expansion of macro 'MAT3' 501 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:500:5: note: in expansion of macro 'MAT3' 500 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:499:5: note: in expansion of macro 'MAT3' 499 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:498:5: note: in expansion of macro 'MAT3' 498 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:497:5: note: in expansion of macro 'MAT3' 497 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:496:5: note: in expansion of macro 'MAT3' 496 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:495:5: note: in expansion of macro 'MAT3' 495 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:494:5: note: in expansion of macro 'MAT3' 494 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:492:5: note: in expansion of macro 'MAT3' 492 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:491:5: note: in expansion of macro 'MAT3' 491 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:490:5: note: in expansion of macro 'MAT3' 490 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:489:5: note: in expansion of macro 'MAT3' 489 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:488:5: note: in expansion of macro 'MAT3' 488 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:486:5: note: in expansion of macro 'MAT3' 486 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:484:5: note: in expansion of macro 'MAT3' 484 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:483:5: note: in expansion of macro 'MAT3' 483 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:482:5: note: in expansion of macro 'MAT3' 482 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:472:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] 472 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:28: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:22: warning: variable 'km2' set but not used [-Wunused-but-set-variable] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:468:28: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] 468 | int jm1, jp1, jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:467:28: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] 467 | int im1, ip1, im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1380:5: note: in expansion of macro 'MAT3' 1380 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1379:5: note: in expansion of macro 'MAT3' 1379 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1378:5: note: in expansion of macro 'MAT3' 1378 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1377:5: note: in expansion of macro 'MAT3' 1377 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1376:5: note: in expansion of macro 'MAT3' 1376 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1375:5: note: in expansion of macro 'MAT3' 1375 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1374:5: note: in expansion of macro 'MAT3' 1374 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1373:5: note: in expansion of macro 'MAT3' 1373 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1372:5: note: in expansion of macro 'MAT3' 1372 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1370:5: note: in expansion of macro 'MAT3' 1370 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1369:5: note: in expansion of macro 'MAT3' 1369 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1368:5: note: in expansion of macro 'MAT3' 1368 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1367:5: note: in expansion of macro 'MAT3' 1367 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1366:5: note: in expansion of macro 'MAT3' 1366 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1365:5: note: in expansion of macro 'MAT3' 1365 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1364:5: note: in expansion of macro 'MAT3' 1364 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1363:5: note: in expansion of macro 'MAT3' 1363 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1362:5: note: in expansion of macro 'MAT3' 1362 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1360:5: note: in expansion of macro 'MAT3' 1360 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1359:5: note: in expansion of macro 'MAT3' 1359 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1358:5: note: in expansion of macro 'MAT3' 1358 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1357:5: note: in expansion of macro 'MAT3' 1357 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1356:5: note: in expansion of macro 'MAT3' 1356 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1355:5: note: in expansion of macro 'MAT3' 1355 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1354:5: note: in expansion of macro 'MAT3' 1354 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1353:5: note: in expansion of macro 'MAT3' 1353 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1352:5: note: in expansion of macro 'MAT3' 1352 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1350:5: note: in expansion of macro 'MAT3' 1350 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1349:5: note: in expansion of macro 'MAT3' 1349 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1348:5: note: in expansion of macro 'MAT3' 1348 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1347:5: note: in expansion of macro 'MAT3' 1347 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1346:5: note: in expansion of macro 'MAT3' 1346 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1345:5: note: in expansion of macro 'MAT3' 1345 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1344:5: note: in expansion of macro 'MAT3' 1344 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1343:5: note: in expansion of macro 'MAT3' 1343 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1342:5: note: in expansion of macro 'MAT3' 1342 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1340:5: note: in expansion of macro 'MAT3' 1340 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1339:5: note: in expansion of macro 'MAT3' 1339 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1338:5: note: in expansion of macro 'MAT3' 1338 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1337:5: note: in expansion of macro 'MAT3' 1337 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1336:5: note: in expansion of macro 'MAT3' 1336 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1334:5: note: in expansion of macro 'MAT3' 1334 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1333:5: note: in expansion of macro 'MAT3' 1333 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1332:5: note: in expansion of macro 'MAT3' 1332 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1331:5: note: in expansion of macro 'MAT3' 1331 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1330:5: note: in expansion of macro 'MAT3' 1330 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1329:5: note: in expansion of macro 'MAT3' 1329 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1328:5: note: in expansion of macro 'MAT3' 1328 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1327:5: note: in expansion of macro 'MAT3' 1327 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1326:5: note: in expansion of macro 'MAT3' 1326 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1324:5: note: in expansion of macro 'MAT3' 1324 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1323:5: note: in expansion of macro 'MAT3' 1323 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1322:5: note: in expansion of macro 'MAT3' 1322 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1321:5: note: in expansion of macro 'MAT3' 1321 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1320:5: note: in expansion of macro 'MAT3' 1320 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1276:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] 1276 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:28: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] 1273 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:22: warning: variable 'km2' set but not used [-Wunused-but-set-variable] 1273 | int km1, kp1, km2, kp2; | ^~~ [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:67:5: note: in expansion of macro 'MAT2' 67 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:66:5: note: in expansion of macro 'MAT2' 66 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_trilin': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:101:5: note: in expansion of macro 'MAT2' 101 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_trilin': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:163:5: note: in expansion of macro 'MAT3' 163 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:162:5: note: in expansion of macro 'MAT3' 162 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:161:5: note: in expansion of macro 'MAT3' 161 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:160:5: note: in expansion of macro 'MAT3' 160 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:158:5: note: in expansion of macro 'MAT3' 158 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:157:5: note: in expansion of macro 'MAT3' 157 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:156:5: note: in expansion of macro 'MAT3' 156 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:155:5: note: in expansion of macro 'MAT3' 155 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:154:5: note: in expansion of macro 'MAT3' 154 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:152:5: note: in expansion of macro 'MAT3' 152 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:151:5: note: in expansion of macro 'MAT3' 151 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:150:5: note: in expansion of macro 'MAT3' 150 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:149:5: note: in expansion of macro 'MAT3' 149 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:147:5: note: in expansion of macro 'MAT3' 147 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:146:5: note: in expansion of macro 'MAT3' 146 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:145:5: note: in expansion of macro 'MAT3' 145 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:144:5: note: in expansion of macro 'MAT3' 144 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:143:5: note: in expansion of macro 'MAT3' 143 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:141:5: note: in expansion of macro 'MAT3' 141 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:140:5: note: in expansion of macro 'MAT3' 140 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:139:5: note: in expansion of macro 'MAT3' 139 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:138:5: note: in expansion of macro 'MAT3' 138 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:136:5: note: in expansion of macro 'MAT3' 136 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:135:5: note: in expansion of macro 'MAT3' 135 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:134:5: note: in expansion of macro 'MAT3' 134 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:133:5: note: in expansion of macro 'MAT3' 133 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:132:5: note: in expansion of macro 'MAT3' 132 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_op7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:212:5: note: in expansion of macro 'MAT2' 212 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:211:5: note: in expansion of macro 'MAT2' 211 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_op7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:287:5: note: in expansion of macro 'MAT3' 287 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:286:5: note: in expansion of macro 'MAT3' 286 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:285:5: note: in expansion of macro 'MAT3' 285 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:284:5: note: in expansion of macro 'MAT3' 284 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:283:5: note: in expansion of macro 'MAT3' 283 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:282:5: note: in expansion of macro 'MAT3' 282 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:281:5: note: in expansion of macro 'MAT3' 281 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:280:5: note: in expansion of macro 'MAT3' 280 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:279:5: note: in expansion of macro 'MAT3' 279 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:278:5: note: in expansion of macro 'MAT3' 278 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:277:5: note: in expansion of macro 'MAT3' 277 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:276:5: note: in expansion of macro 'MAT3' 276 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:275:5: note: in expansion of macro 'MAT3' 275 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:274:5: note: in expansion of macro 'MAT3' 274 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:273:5: note: in expansion of macro 'MAT3' 273 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:272:5: note: in expansion of macro 'MAT3' 272 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:271:5: note: in expansion of macro 'MAT3' 271 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:270:5: note: in expansion of macro 'MAT3' 270 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:269:5: note: in expansion of macro 'MAT3' 269 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:268:5: note: in expansion of macro 'MAT3' 268 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:267:5: note: in expansion of macro 'MAT3' 267 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:266:5: note: in expansion of macro 'MAT3' 266 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:265:5: note: in expansion of macro 'MAT3' 265 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:264:5: note: in expansion of macro 'MAT3' 264 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:263:5: note: in expansion of macro 'MAT3' 263 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:262:5: note: in expansion of macro 'MAT3' 262 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:261:5: note: in expansion of macro 'MAT3' 261 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:260:5: note: in expansion of macro 'MAT3' 260 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:259:5: note: in expansion of macro 'MAT3' 259 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:258:5: note: in expansion of macro 'MAT3' 258 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:257:5: note: in expansion of macro 'MAT3' 257 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:32: warning: variable 'eighth' set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:23: warning: variable 'quarter' set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:17: warning: variable 'half' set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:15: warning: variable 'kkp1' set but not used [-Wunused-but-set-variable] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:15: warning: variable 'jjp1' set but not used [-Wunused-but-set-variable] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:9: warning: variable 'jjm1' set but not used [-Wunused-but-set-variable] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:15: warning: variable 'iip1' set but not used [-Wunused-but-set-variable] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:9: warning: variable 'iim1' set but not used [-Wunused-but-set-variable] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:16: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:10: warning: variable 'km2' set but not used [-Wunused-but-set-variable] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:16: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:10: warning: variable 'jm2' set but not used [-Wunused-but-set-variable] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:16: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:10: warning: variable 'im2' set but not used [-Wunused-but-set-variable] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_op27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:728:5: note: in expansion of macro 'MAT2' 728 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:727:5: note: in expansion of macro 'MAT2' 727 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_op27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:818:7: note: in expansion of macro 'MAT3' 818 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:817:7: note: in expansion of macro 'MAT3' 817 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:816:7: note: in expansion of macro 'MAT3' 816 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:815:7: note: in expansion of macro 'MAT3' 815 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:814:7: note: in expansion of macro 'MAT3' 814 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:813:7: note: in expansion of macro 'MAT3' 813 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:812:7: note: in expansion of macro 'MAT3' 812 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:811:7: note: in expansion of macro 'MAT3' 811 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:810:7: note: in expansion of macro 'MAT3' 810 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:809:7: note: in expansion of macro 'MAT3' 809 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:808:7: note: in expansion of macro 'MAT3' 808 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:807:7: note: in expansion of macro 'MAT3' 807 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:806:7: note: in expansion of macro 'MAT3' 806 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:805:7: note: in expansion of macro 'MAT3' 805 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:804:7: note: in expansion of macro 'MAT3' 804 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:803:7: note: in expansion of macro 'MAT3' 803 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:802:7: note: in expansion of macro 'MAT3' 802 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:801:7: note: in expansion of macro 'MAT3' 801 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:800:7: note: in expansion of macro 'MAT3' 800 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:799:7: note: in expansion of macro 'MAT3' 799 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:798:7: note: in expansion of macro 'MAT3' 798 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:797:7: note: in expansion of macro 'MAT3' 797 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:796:7: note: in expansion of macro 'MAT3' 796 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:795:7: note: in expansion of macro 'MAT3' 795 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:794:7: note: in expansion of macro 'MAT3' 794 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:793:7: note: in expansion of macro 'MAT3' 793 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:792:7: note: in expansion of macro 'MAT3' 792 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:791:7: note: in expansion of macro 'MAT3' 791 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:790:7: note: in expansion of macro 'MAT3' 790 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:789:7: note: in expansion of macro 'MAT3' 789 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:788:7: note: in expansion of macro 'MAT3' 788 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:787:7: note: in expansion of macro 'MAT3' 787 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:786:7: note: in expansion of macro 'MAT3' 786 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:785:7: note: in expansion of macro 'MAT3' 785 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:784:7: note: in expansion of macro 'MAT3' 784 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:783:7: note: in expansion of macro 'MAT3' 783 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:782:7: note: in expansion of macro 'MAT3' 782 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:781:7: note: in expansion of macro 'MAT3' 781 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:780:7: note: in expansion of macro 'MAT3' 780 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:779:7: note: in expansion of macro 'MAT3' 779 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:778:7: note: in expansion of macro 'MAT3' 778 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:34: warning: variable 'eighth' set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:25: warning: variable 'quarter' set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:19: warning: variable 'half' set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:17: warning: variable 'kkp1' set but not used [-Wunused-but-set-variable] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:11: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:17: warning: variable 'jjp1' set but not used [-Wunused-but-set-variable] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:11: warning: variable 'jjm1' set but not used [-Wunused-but-set-variable] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:17: warning: variable 'iip1' set but not used [-Wunused-but-set-variable] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:11: warning: variable 'iim1' set but not used [-Wunused-but-set-variable] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:18: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:12: warning: variable 'km2' set but not used [-Wunused-but-set-variable] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:18: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:12: warning: variable 'jm2' set but not used [-Wunused-but-set-variable] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:18: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] 767 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:12: warning: variable 'im2' set but not used [-Wunused-but-set-variable] 767 | int im2, ip2; | ^~~ [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c: In function 'Vcghs': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c:99:24: warning: 'rhok1' may be used uninitialized [-Wmaybe-uninitialized] 99 | beta = rhok2 / rhok1; | ~~~~~~^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c:66:12: note: 'rhok1' was declared here 66 | double rhok1, rhok2, alpha, beta; | ^~~~~ [ 33%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:67:5: note: in expansion of macro 'MAT2' 67 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb7x': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:116:5: note: in expansion of macro 'MAT3' 116 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:115:5: note: in expansion of macro 'MAT3' 115 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:114:5: note: in expansion of macro 'MAT3' 114 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:113:5: note: in expansion of macro 'MAT3' 113 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_r' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_r' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w2' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w2' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w2' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w1' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w1' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:108:5: note: in expansion of macro 'MAT3' 108 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:107:5: note: in expansion of macro 'MAT3' 107 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:106:5: note: in expansion of macro 'MAT3' 106 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb27x': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:208:5: note: in expansion of macro 'MAT3' 208 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:207:5: note: in expansion of macro 'MAT3' 207 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:206:5: note: in expansion of macro 'MAT3' 206 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:205:5: note: in expansion of macro 'MAT3' 205 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:204:5: note: in expansion of macro 'MAT3' 204 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:203:5: note: in expansion of macro 'MAT3' 203 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:202:5: note: in expansion of macro 'MAT3' 202 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:201:5: note: in expansion of macro 'MAT3' 201 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:199:5: note: in expansion of macro 'MAT3' 199 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:198:5: note: in expansion of macro 'MAT3' 198 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:196:5: note: in expansion of macro 'MAT3' 196 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:195:5: note: in expansion of macro 'MAT3' 195 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:194:5: note: in expansion of macro 'MAT3' 194 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:193:5: note: in expansion of macro 'MAT3' 193 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_r' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_r' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w2' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w2' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w2' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w1' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w1' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:188:5: note: in expansion of macro 'MAT3' 188 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:187:5: note: in expansion of macro 'MAT3' 187 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:186:5: note: in expansion of macro 'MAT3' 186 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:182:9: warning: variable 'istep' set but not used [-Wunused-but-set-variable] 182 | int istep; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:17: warning: variable 'k2' set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:13: warning: variable 'j2' set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:9: warning: variable 'i2' set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:17: warning: variable 'k1' set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:13: warning: variable 'j1' set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:9: warning: variable 'i1' set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ [ 34%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h:55, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:87:5: note: in expansion of macro 'MAT2' 87 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:112:5: note: in expansion of macro 'MAT3' 112 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:111:5: note: in expansion of macro 'MAT3' 111 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:110:5: note: in expansion of macro 'MAT3' 110 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:109:5: note: in expansion of macro 'MAT3' 109 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:108:5: note: in expansion of macro 'MAT3' 108 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:107:5: note: in expansion of macro 'MAT3' 107 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:106:5: note: in expansion of macro 'MAT3' 106 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:139:5: note: in expansion of macro 'MAT2' 139 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:184:5: note: in expansion of macro 'MAT3' 184 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:183:5: note: in expansion of macro 'MAT3' 183 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:182:5: note: in expansion of macro 'MAT3' 182 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:181:5: note: in expansion of macro 'MAT3' 181 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:180:5: note: in expansion of macro 'MAT3' 180 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:179:5: note: in expansion of macro 'MAT3' 179 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:178:5: note: in expansion of macro 'MAT3' 178 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:177:5: note: in expansion of macro 'MAT3' 177 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:176:5: note: in expansion of macro 'MAT3' 176 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:174:5: note: in expansion of macro 'MAT3' 174 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:173:5: note: in expansion of macro 'MAT3' 173 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:172:5: note: in expansion of macro 'MAT3' 172 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:171:5: note: in expansion of macro 'MAT3' 171 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:170:5: note: in expansion of macro 'MAT3' 170 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:168:5: note: in expansion of macro 'MAT3' 168 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:167:5: note: in expansion of macro 'MAT3' 167 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:166:5: note: in expansion of macro 'MAT3' 166 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvec7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:263:5: note: in expansion of macro 'MAT2' 263 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvecd7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:292:5: note: in expansion of macro 'MAT3' 292 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:291:5: note: in expansion of macro 'MAT3' 291 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:290:5: note: in expansion of macro 'MAT3' 290 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:289:5: note: in expansion of macro 'MAT3' 289 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:287:5: note: in expansion of macro 'MAT3' 287 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:286:5: note: in expansion of macro 'MAT3' 286 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:285:5: note: in expansion of macro 'MAT3' 285 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvec27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:322:5: note: in expansion of macro 'MAT2' 322 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvecd27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:370:5: note: in expansion of macro 'MAT3' 370 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:369:5: note: in expansion of macro 'MAT3' 369 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:368:5: note: in expansion of macro 'MAT3' 368 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:367:5: note: in expansion of macro 'MAT3' 367 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:365:5: note: in expansion of macro 'MAT3' 365 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:364:5: note: in expansion of macro 'MAT3' 364 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:363:5: note: in expansion of macro 'MAT3' 363 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:362:5: note: in expansion of macro 'MAT3' 362 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:361:5: note: in expansion of macro 'MAT3' 361 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:360:5: note: in expansion of macro 'MAT3' 360 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:359:5: note: in expansion of macro 'MAT3' 359 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:358:5: note: in expansion of macro 'MAT3' 358 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:357:5: note: in expansion of macro 'MAT3' 357 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:356:5: note: in expansion of macro 'MAT3' 356 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:355:5: note: in expansion of macro 'MAT3' 355 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:354:5: note: in expansion of macro 'MAT3' 354 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:353:5: note: in expansion of macro 'MAT3' 353 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:451:5: note: in expansion of macro 'MAT2' 451 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:476:5: note: in expansion of macro 'MAT3' 476 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:475:5: note: in expansion of macro 'MAT3' 475 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:474:5: note: in expansion of macro 'MAT3' 474 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:473:5: note: in expansion of macro 'MAT3' 473 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:472:5: note: in expansion of macro 'MAT3' 472 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:471:5: note: in expansion of macro 'MAT3' 471 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:470:5: note: in expansion of macro 'MAT3' 470 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:469:5: note: in expansion of macro 'MAT3' 469 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:503:5: note: in expansion of macro 'MAT2' 503 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:550:5: note: in expansion of macro 'MAT3' 550 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:549:5: note: in expansion of macro 'MAT3' 549 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:548:5: note: in expansion of macro 'MAT3' 548 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:547:5: note: in expansion of macro 'MAT3' 547 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:546:5: note: in expansion of macro 'MAT3' 546 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:545:5: note: in expansion of macro 'MAT3' 545 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:544:5: note: in expansion of macro 'MAT3' 544 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:543:5: note: in expansion of macro 'MAT3' 543 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:542:5: note: in expansion of macro 'MAT3' 542 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:540:5: note: in expansion of macro 'MAT3' 540 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:539:5: note: in expansion of macro 'MAT3' 539 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:538:5: note: in expansion of macro 'MAT3' 538 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:537:5: note: in expansion of macro 'MAT3' 537 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:536:5: note: in expansion of macro 'MAT3' 536 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:534:5: note: in expansion of macro 'MAT3' 534 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:533:5: note: in expansion of macro 'MAT3' 533 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:532:5: note: in expansion of macro 'MAT3' 532 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:531:5: note: in expansion of macro 'MAT3' 531 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:623:5: note: in expansion of macro 'MAT2' 623 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:650:5: note: in expansion of macro 'MAT3' 650 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:649:5: note: in expansion of macro 'MAT3' 649 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:648:5: note: in expansion of macro 'MAT3' 648 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:647:5: note: in expansion of macro 'MAT3' 647 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:646:5: note: in expansion of macro 'MAT3' 646 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:644:5: note: in expansion of macro 'MAT3' 644 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:643:5: note: in expansion of macro 'MAT3' 643 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:642:5: note: in expansion of macro 'MAT3' 642 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:681:5: note: in expansion of macro 'MAT2' 681 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:727:5: note: in expansion of macro 'MAT3' 727 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:726:5: note: in expansion of macro 'MAT3' 726 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:725:5: note: in expansion of macro 'MAT3' 725 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:724:5: note: in expansion of macro 'MAT3' 724 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:723:5: note: in expansion of macro 'MAT3' 723 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:722:5: note: in expansion of macro 'MAT3' 722 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:721:5: note: in expansion of macro 'MAT3' 721 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:720:5: note: in expansion of macro 'MAT3' 720 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:719:5: note: in expansion of macro 'MAT3' 719 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:718:5: note: in expansion of macro 'MAT3' 718 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:717:5: note: in expansion of macro 'MAT3' 717 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:716:5: note: in expansion of macro 'MAT3' 716 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:715:5: note: in expansion of macro 'MAT3' 715 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:714:5: note: in expansion of macro 'MAT3' 714 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:713:5: note: in expansion of macro 'MAT3' 713 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:712:5: note: in expansion of macro 'MAT3' 712 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:711:5: note: in expansion of macro 'MAT3' 711 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:709:5: note: in expansion of macro 'MAT3' 709 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vrestrc': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:786:5: note: in expansion of macro 'MAT2' 786 | MAT2(pc, *nxc * *nyc * *nzc, 1 ); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vrestrc2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:852:5: note: in expansion of macro 'MAT3' 852 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:851:5: note: in expansion of macro 'MAT3' 851 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:850:5: note: in expansion of macro 'MAT3' 850 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:849:5: note: in expansion of macro 'MAT3' 849 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:847:5: note: in expansion of macro 'MAT3' 847 | MAT3(dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:846:5: note: in expansion of macro 'MAT3' 846 | MAT3(dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:845:5: note: in expansion of macro 'MAT3' 845 | MAT3(dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:844:5: note: in expansion of macro 'MAT3' 844 | MAT3(dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:843:5: note: in expansion of macro 'MAT3' 843 | MAT3(dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:841:5: note: in expansion of macro 'MAT3' 841 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:840:5: note: in expansion of macro 'MAT3' 840 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:839:5: note: in expansion of macro 'MAT3' 839 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:838:5: note: in expansion of macro 'MAT3' 838 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:836:5: note: in expansion of macro 'MAT3' 836 | MAT3(uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:835:5: note: in expansion of macro 'MAT3' 835 | MAT3(uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:834:5: note: in expansion of macro 'MAT3' 834 | MAT3(uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:833:5: note: in expansion of macro 'MAT3' 833 | MAT3(uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:832:5: note: in expansion of macro 'MAT3' 832 | MAT3(uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:830:5: note: in expansion of macro 'MAT3' 830 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:829:5: note: in expansion of macro 'MAT3' 829 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:828:5: note: in expansion of macro 'MAT3' 828 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:827:5: note: in expansion of macro 'MAT3' 827 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:825:5: note: in expansion of macro 'MAT3' 825 | MAT3(oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:824:5: note: in expansion of macro 'MAT3' 824 | MAT3(oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:823:5: note: in expansion of macro 'MAT3' 823 | MAT3(oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:822:5: note: in expansion of macro 'MAT3' 822 | MAT3(oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:821:5: note: in expansion of macro 'MAT3' 821 | MAT3(oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:819:5: note: in expansion of macro 'MAT3' 819 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:818:5: note: in expansion of macro 'MAT3' 818 | MAT3(xin, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:816:12: warning: variable 'dimfac' set but not used [-Wunused-but-set-variable] 816 | double dimfac; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'VinterpPMG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:920:5: note: in expansion of macro 'MAT2' 920 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'VinterpPMG2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:982:5: note: in expansion of macro 'MAT3' 982 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:981:5: note: in expansion of macro 'MAT3' 981 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:980:5: note: in expansion of macro 'MAT3' 980 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:979:5: note: in expansion of macro 'MAT3' 979 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:977:5: note: in expansion of macro 'MAT3' 977 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:976:5: note: in expansion of macro 'MAT3' 976 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:975:5: note: in expansion of macro 'MAT3' 975 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:974:5: note: in expansion of macro 'MAT3' 974 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:973:5: note: in expansion of macro 'MAT3' 973 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:971:5: note: in expansion of macro 'MAT3' 971 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:970:5: note: in expansion of macro 'MAT3' 970 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:969:5: note: in expansion of macro 'MAT3' 969 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:968:5: note: in expansion of macro 'MAT3' 968 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:966:5: note: in expansion of macro 'MAT3' 966 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:965:5: note: in expansion of macro 'MAT3' 965 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:964:5: note: in expansion of macro 'MAT3' 964 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:963:5: note: in expansion of macro 'MAT3' 963 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:962:5: note: in expansion of macro 'MAT3' 962 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:960:5: note: in expansion of macro 'MAT3' 960 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:959:5: note: in expansion of macro 'MAT3' 959 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:958:5: note: in expansion of macro 'MAT3' 958 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:957:5: note: in expansion of macro 'MAT3' 957 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:955:5: note: in expansion of macro 'MAT3' 955 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:954:5: note: in expansion of macro 'MAT3' 954 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:953:5: note: in expansion of macro 'MAT3' 953 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:952:5: note: in expansion of macro 'MAT3' 952 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_oPC' [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_oPC' [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:949:5: note: in expansion of macro 'MAT3' 949 | MAT3(xout, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:948:5: note: in expansion of macro 'MAT3' 948 | MAT3( xin, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vextrac': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1086:5: note: in expansion of macro 'MAT3' 1086 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1085:5: note: in expansion of macro 'MAT3' 1085 | MAT3( xin, *nxf, *nyf, *nzf); | ^~~~ [ 35%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c: In function 'Vmvcs': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:99:5: note: in expansion of macro 'MAT2' 99 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:562:37: warning: 'rsden' may be used uninitialized [-Wmaybe-uninitialized] 562 | } while (*iters<*itmax && (rsnrm/rsden) > *errtol); | ~~~~~~^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:88:12: note: 'rsden' was declared here 88 | double rsden; // @todo: doc | ^~~~~ [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgdriv': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:85:9: warning: unused variable 'ierror' [-Wunused-variable] 85 | int ierror = 0; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h:62, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgdriv2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:267:5: note: in expansion of macro 'MAT2' 267 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:234:12: warning: unused variable 'tsolve' [-Wunused-variable] 234 | double tsolve = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:233:12: warning: unused variable 'tsetupc' [-Wunused-variable] 233 | double tsetupc = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:232:12: warning: unused variable 'tsetupf' [-Wunused-variable] 232 | double tsetupf = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:231:12: warning: unused variable 'oh' [-Wunused-variable] 231 | double oh = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:230:12: warning: unused variable 'bf' [-Wunused-variable] 230 | double bf = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:226:12: warning: unused variable 'epsmac' [-Wunused-variable] 226 | double epsmac = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgsz': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:655:26: warning: 'num_narrc_oper' may be used uninitialized [-Wmaybe-uninitialized] 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:580:22: note: 'num_narrc_oper' was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:656:13: warning: 'n_band' may be used uninitialized [-Wmaybe-uninitialized] 653 | *iretot = num_narr * *narr | ~~~~~~~~~~~~~~~~ 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 656 | + n_band | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:577:28: note: 'n_band' was declared here 577 | int nc_band, num_band, n_band; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:654:41: warning: 'num_nf_oper' may be used uninitialized [-Wmaybe-uninitialized] 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:580:9: note: 'num_nf_oper' was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~ [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildops': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:83:5: note: in expansion of macro 'MAT2' 83 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildstr': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:266:5: note: in expansion of macro 'MAT2' 266 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildcopy0': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:628:5: note: in expansion of macro 'MAT3' 628 | MAT3( fcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_ccf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:627:5: note: in expansion of macro 'MAT3' 627 | MAT3( ccf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_tcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:626:5: note: in expansion of macro 'MAT3' 626 | MAT3( tcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:625:5: note: in expansion of macro 'MAT3' 625 | MAT3(a3cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:624:5: note: in expansion of macro 'MAT3' 624 | MAT3(a2cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1cf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:623:5: note: in expansion of macro 'MAT3' 623 | MAT3(a1cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:622:5: note: in expansion of macro 'MAT3' 622 | MAT3(gzcf, *nxf, *nyf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gycf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:621:5: note: in expansion of macro 'MAT3' 621 | MAT3(gycf, *nxf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxcf' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:620:5: note: in expansion of macro 'MAT3' 620 | MAT3(gxcf, *nyf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_tc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:619:5: note: in expansion of macro 'MAT3' 619 | MAT3( tc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:618:5: note: in expansion of macro 'MAT3' 618 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:617:5: note: in expansion of macro 'MAT3' 617 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3c' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:616:5: note: in expansion of macro 'MAT3' 616 | MAT3( a3c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2c' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:615:5: note: in expansion of macro 'MAT3' 615 | MAT3( a2c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1c' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:614:5: note: in expansion of macro 'MAT3' 614 | MAT3( a1c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:613:5: note: in expansion of macro 'MAT3' 613 | MAT3( gzc, *nx, *ny, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gyc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:612:5: note: in expansion of macro 'MAT3' 612 | MAT3( gyc, *nx, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:611:5: note: in expansion of macro 'MAT3' 611 | MAT3( gxc, *ny, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildalg': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:914:5: note: in expansion of macro 'MAT2' 914 | MAT2(iz, 50, *nlev); | ^~~~ [ 39%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:60:5: note: in expansion of macro 'MAT3' 60 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:59:5: note: in expansion of macro 'MAT3' 59 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy_small': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:78:5: note: in expansion of macro 'MAT3' 78 | MAT3(y, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:77:5: note: in expansion of macro 'MAT3' 77 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy_large': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:99:5: note: in expansion of macro 'MAT3' 99 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:98:5: note: in expansion of macro 'MAT3' 98 | MAT3(x, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxaxpy': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:117:5: note: in expansion of macro 'MAT3' 117 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:116:5: note: in expansion of macro 'MAT3' 116 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxnrm1': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:136:5: note: in expansion of macro 'MAT3' 136 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxnrm2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:157:5: note: in expansion of macro 'MAT3' 157 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxdot': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:182:5: note: in expansion of macro 'MAT3' 182 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:181:5: note: in expansion of macro 'MAT3' 181 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vazeros': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:198:9: warning: unused variable 'nproc' [-Wunused-variable] 198 | int nproc = 1; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'VfboundPMG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:218:5: note: in expansion of macro 'MAT3' 218 | MAT3(gzc, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gyc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:217:5: note: in expansion of macro 'MAT3' 217 | MAT3(gyc, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxc' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:216:5: note: in expansion of macro 'MAT3' 216 | MAT3(gxc, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:215:5: note: in expansion of macro 'MAT3' 215 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'VfboundPMG00': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:262:5: note: in expansion of macro 'MAT3' 262 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vaxrand': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:295:12: warning: variable 'xdum' set but not used [-Wunused-but-set-variable] 295 | double xdum; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:33: warning: variable 'iflag' set but not used [-Wunused-but-set-variable] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:26: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxscal': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:322:5: note: in expansion of macro 'MAT3' 322 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:337:5: note: in expansion of macro 'MAT2' 337 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:370:5: note: in expansion of macro 'MAT3' 370 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:369:5: note: in expansion of macro 'MAT3' 369 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:368:5: note: in expansion of macro 'MAT3' 368 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:367:5: note: in expansion of macro 'MAT3' 367 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:415:5: note: in expansion of macro 'MAT3' 415 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:414:5: note: in expansion of macro 'MAT3' 414 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:413:5: note: in expansion of macro 'MAT3' 413 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:412:5: note: in expansion of macro 'MAT3' 412 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:411:5: note: in expansion of macro 'MAT3' 411 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:410:5: note: in expansion of macro 'MAT3' 410 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:409:5: note: in expansion of macro 'MAT3' 409 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:408:5: note: in expansion of macro 'MAT3' 408 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:407:5: note: in expansion of macro 'MAT3' 407 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:406:5: note: in expansion of macro 'MAT3' 406 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:405:5: note: in expansion of macro 'MAT3' 405 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:404:5: note: in expansion of macro 'MAT3' 404 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:403:5: note: in expansion of macro 'MAT3' 403 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:402:5: note: in expansion of macro 'MAT3' 402 | MAT3( oC, *nx, *ny, *nz); | ^~~~ [ 40%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function 'Vdpbsl': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_abd' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:62:5: note: in expansion of macro 'MAT2' 62 | MAT2(abd, *lda, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function 'Vdpbfa': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_abd' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:199:5: note: in expansion of macro 'MAT2' 199 | MAT2(abd, *lda, 1); | ^~~~ [ 41%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vmypdefinitsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:96:9: warning: unused variable 'i' [-Wunused-variable] 96 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vc_vecsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:26: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:19: warning: variable 'ipara' set but not used [-Wunused-but-set-variable] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:15: warning: unused variable 'ii' [-Wunused-variable] 223 | int n, i, ii, ipara, ivect; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:222:9: warning: unused variable 'iion' [-Wunused-variable] 222 | int iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:28: warning: unused variable 'fact' [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:22: warning: unused variable 'poly' [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:12: warning: unused variable 'argument' [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:29: warning: unused variable 'am_pos' [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:21: warning: unused variable 'am_neg' [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:18: warning: unused variable 'zu2' [-Wunused-variable] 217 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:12: warning: unused variable 'zcf2' [-Wunused-variable] 217 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:216:9: warning: unused variable 'ideg' [-Wunused-variable] 216 | int ideg; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vec': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:345:9: warning: unused variable 'n' [-Wunused-variable] 345 | int n = *nx * *ny * *nz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:344:9: warning: unused variable 'i' [-Wunused-variable] 344 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vecpmg': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:28: warning: unused variable 'fact' [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:22: warning: unused variable 'poly' [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:357:9: warning: unused variable 'ideg' [-Wunused-variable] 357 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vecsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:16: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:9: warning: variable 'ipara' set but not used [-Wunused-but-set-variable] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:432:15: warning: unused variable 'ii' [-Wunused-variable] 432 | int n, i, ii; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:28: warning: unused variable 'fact' [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:22: warning: unused variable 'poly' [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:12: warning: unused variable 'argument' [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:29: warning: unused variable 'am_pos' [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:21: warning: unused variable 'am_neg' [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:18: warning: unused variable 'zu2' [-Wunused-variable] 427 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:12: warning: unused variable 'zcf2' [-Wunused-variable] 427 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:15: warning: unused variable 'iion' [-Wunused-variable] 426 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:9: warning: unused variable 'ideg' [-Wunused-variable] 426 | int ideg, iion; | ^~~~ [ 42%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:56: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vfnewton': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:77:5: note: in expansion of macro 'MAT2' 77 | MAT2( iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vnewton': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:187:5: note: in expansion of macro 'MAT2' 187 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vgetjac': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:560:5: note: in expansion of macro 'MAT2' 560 | MAT2(iz, 50, 1); | ^~~~ [ 43%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function 'Vnewdriv': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:86:9: warning: unused variable 'maxlev' [-Wunused-variable] 86 | int maxlev; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:85:9: warning: unused variable 'ierror' [-Wunused-variable] 85 | int ierror; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function 'Vnewdriv2': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:223:9: warning: unused variable 'i' [-Wunused-variable] 223 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:221:12: warning: unused variable 'orsnrm_t' [-Wunused-variable] 221 | double orsnrm_t; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:220:12: warning: unused variable 'rsden_t' [-Wunused-variable] 220 | double rsden_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:219:12: warning: unused variable 'rsnrm_t' [-Wunused-variable] 219 | double rsnrm_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:218:9: warning: unused variable 'iters_t' [-Wunused-variable] 218 | int iters_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:217:9: warning: unused variable 'iok_t' [-Wunused-variable] 217 | int iok_t; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:215:9: warning: unused variable 'numlev' [-Wunused-variable] 215 | int numlev; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:210:12: warning: unused variable 'tsolve' [-Wunused-variable] 210 | double tsolve; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:209:12: warning: unused variable 'tsetupc' [-Wunused-variable] 209 | double tsetupc; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:208:12: warning: unused variable 'tsetupf' [-Wunused-variable] 208 | double tsetupf; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:207:12: warning: unused variable 'oh' [-Wunused-variable] 207 | double oh; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:206:12: warning: unused variable 'bf' [-Wunused-variable] 206 | double bf; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:204:12: warning: variable 'omegal' set but not used [-Wunused-but-set-variable] 204 | double omegal; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:202:12: warning: unused variable 'epsmac' [-Wunused-variable] 202 | double epsmac; /// @todo: Doc | ^~~~~~ [ 44%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vpower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:74:5: note: in expansion of macro 'MAT2' 74 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:71:9: warning: unused variable 'skipIters' [-Wunused-variable] 71 | int skipIters = 0; | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vipower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:188:5: note: in expansion of macro 'MAT2' 188 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vmpower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:311:5: note: in expansion of macro 'MAT2' 311 | MAT2(iz, 50, 1); | ^~~~ [ 45%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o [ 47%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function 'Vfmvfas': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:79:5: note: in expansion of macro 'MAT2' 79 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:74:12: warning: variable 'errd' set but not used [-Wunused-but-set-variable] 74 | double errd; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function 'Vmvfas': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:182:5: note: in expansion of macro 'MAT2' 182 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:171:33: warning: unused variable 'ivariv' [-Wunused-variable] 171 | int itmax_s, iters_s, nuuu, ivariv, mgsmoo_s, iresid; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:597:24: warning: 'rsden' may be used uninitialized [-Wmaybe-uninitialized] 597 | if ((rsnrm / rsden) <= *errtol) | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:176:12: note: 'rsden' was declared here 176 | double rsden, rsnrm, orsnrm; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 47%] Built target apbs_pmgc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 48%] Linking C shared library ../lib/libapbs.so make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 48%] Built target apbs make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 49%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'loadDielMaps': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable 'iparm' set but not used [-Wunused-but-set-variable] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'energyMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable 'mgparm' set but not used [-Wunused-but-set-variable] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable 'mxtype' set but not used [-Wunused-but-set-variable] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolForce': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable 'scalar' set but not used [-Wunused-but-set-variable] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable 'temp' set but not used [-Wunused-but-set-variable] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable 'sav' set but not used [-Wunused-but-set-variable] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable 'sasa' set but not used [-Wunused-but-set-variable] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable 'ts' [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'forceAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable 'apos' [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable 'ts_sub' [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:34: warning: '-PE' directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:30: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writematMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataFlat': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2105:33: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: note: 'scalar' was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataXML': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2363:33: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: note: 'scalar' was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:38: warning: '%s' directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:30: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:38: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:38: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'returnEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2778:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: note: 'scalar' was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2839:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: note: 'scalar' was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printElecEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2904:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: note: 'scalar' was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:18: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2925:12: note: 'scalar' was declared here 2925 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4547:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4547 | disp[0] = (x - center[0]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4548:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4548 | disp[1] = (y - center[1]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4549:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4549 | disp[2] = (z - center[2]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 49%] Built target apbs_routines make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 50%] Building C object src/CMakeFiles/apbs-bin.dir/main.c.o /builddir/build/BUILD/apbs-3.0.0/src/main.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/src/main.c:117:11: warning: unused variable 'gm' [-Wunused-variable] 117 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:116:11: warning: variable 'fetk' set but not used [-Wunused-but-set-variable] 116 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:96:18: warning: unused variable 'geoflowparm' [-Wunused-variable] 96 | GEOFLOWparm *geoflowparm = VNULL; | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:92:14: warning: unused variable 'feparm' [-Wunused-variable] 92 | FEMparm *feparm = VNULL; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:86:17: warning: unused variable 'te' [-Wunused-variable] 86 | clock_t ts, te; | ^~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 51%] Building C object src/CMakeFiles/apbs-bin.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'loadDielMaps': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable 'iparm' set but not used [-Wunused-but-set-variable] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'energyMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable 'mgparm' set but not used [-Wunused-but-set-variable] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable 'mxtype' set but not used [-Wunused-but-set-variable] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolForce': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable 'scalar' set but not used [-Wunused-but-set-variable] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable 'temp' set but not used [-Wunused-but-set-variable] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable 'sav' set but not used [-Wunused-but-set-variable] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable 'sasa' set but not used [-Wunused-but-set-variable] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable 'ts' [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'forceAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable 'apos' [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable 'ts_sub' [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:34: warning: '-PE' directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:30: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writematMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataFlat': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2105:33: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: note: 'scalar' was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataXML': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2363:33: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: note: 'scalar' was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:38: warning: '%s' directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:30: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:38: warning: '%s' directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:38: warning: '%s' directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:38: warning: '%s' directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function 'sprintf', inlined from 'writedataMG' at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'returnEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2778:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: note: 'scalar' was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2839:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: note: 'scalar' was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printElecEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2904:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: note: 'scalar' was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:18: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2925:12: note: 'scalar' was declared here 2925 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4547:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4547 | disp[0] = (x - center[0]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4548:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4548 | disp[1] = (y - center[1]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4549:30: warning: 'center' may be used uninitialized [-Wmaybe-uninitialized] 4549 | disp[2] = (z - center[2]); | ~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4516:12: note: 'center' declared here 4516 | center[3], /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ [ 52%] Linking C executable ../bin/apbs /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function 'Vparam_getAtomData' 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 52%] Built target apbs-bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Generating documentation with Doxygen warning: Tag 'TCL_SUBST' at line 213 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 857 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1313 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1565 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1577 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1586 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' does not exist warning: source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' is not a readable file or directory... skipping. Doxygen version used: 1.9.4 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/fem Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/generic Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/mg Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/pmgc Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.h... 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Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/myp/builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.h:7: warning: the name 'beparm.h' supplied as the argument in the \file statement is not an input file kpathsea: Running mktexfmt latex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.texlive2021/texmf-config/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.texlive2021/texmf-var/web2c mktexfmt [INFO]: --- remaking latex with pdftex mktexfmt: running `pdftex -ini -jobname=latex -progname=latex -translate-file=cp227.tcx *latex.ini' ... This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (INITEX) restricted \write18 enabled. (/usr/share/texlive/texmf-dist/web2c/cp227.tcx) entering extended mode (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/latex.ini (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex) (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. Defining UNIX/DOS style filename parser. catcodes, registers, parameters, LaTeX2e <2020-10-01> patch level 4 (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.ltx (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3-code.tex (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/l3deprecation.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.ltx (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse-generic.tex)) hacks, control, par, spacing, files, font encodings, lengths, ==================================== Local config file fonttext.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmss.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmtt.fd))) ==================================== Local config file fontmath.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmm.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmsy.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omxcmex.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ucmr.fd))) ==================================== Local config file preload.cfg used ===================================== (/usr/share/texlive/texmf-dist/tex/latex/base/preload.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/preload.ltx)) page nos., x-ref, environments, center, verbatim, math definitions, boxes, title, sectioning, contents, floats, footnotes, index, bibliography, output, =========================================== Local configuration file hyphen.cfg used =========================================== (/usr/share/texlive/texmf-dist/tex/generic/babel/hyphen.cfg (/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/dumyhyph.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/zerohyph.tex)) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/share/texlive/texmf-dist/tex/latex/firstaid/latex2e-first-aid-for-externa l-files.ltx) ) ) Beginning to dump on file latex.fmt (preloaded format=latex 2022.7.20) 19193 strings of total length 344823 280635 memory locations dumped; current usage is 165&279279 17486 multiletter control sequences \font\nullfont=nullfont \font\c__fp_exp_intarray=cmr10 at 0.00002pt \font\c__fp_trig_intarray=cmr10 at 0.00003pt \font\c_initex_cctab=cmr10 at 0.00005pt \font\c_other_cctab=cmr10 at 0.00006pt \font\c_str_cctab=cmr10 at 0.00008pt \font\g__regex_state_active_intarray=cmr10 at 0.00009pt \font\g__regex_thread_info_intarray=cmr10 at 0.0001pt \font\g__regex_submatch_prev_intarray=cmr10 at 0.00012pt \font\g__regex_submatch_begin_intarray=cmr10 at 0.00014pt \font\g__regex_submatch_end_intarray=cmr10 at 0.00015pt \font\g__regex_balance_intarray=cmr10 at 0.00017pt \font\OMX/cmex/m/n/10=cmex10 \font\tenln=line10 \font\tenlnw=linew10 \font\tencirc=lcircle10 \font\tencircw=lcirclew10 \font\OT1/cmr/m/n/5=cmr5 \font\OT1/cmr/m/n/7=cmr7 \font\OT1/cmr/m/n/10=cmr10 \font\OML/cmm/m/it/5=cmmi5 \font\OML/cmm/m/it/7=cmmi7 \font\OML/cmm/m/it/10=cmmi10 \font\OMS/cmsy/m/n/5=cmsy5 \font\OMS/cmsy/m/n/7=cmsy7 \font\OMS/cmsy/m/n/10=cmsy10 \font\c_code_cctab=cmr10 at 0.00018pt \font\c_document_cctab=cmr10 at 0.0002pt 403423 words of font info for 27 preloaded fonts 14 hyphenation exceptions Hyphenation trie of length 6081 has 183 ops out of 35111 2 for language 1 181 for language 0 0 words of pdfTeX memory 0 indirect objects No pages of output. Transcript written on latex.log. mktexfmt [INFO]: log file copied to: /builddir/.texlive2021/texmf-var/web2c/pdftex/latex.log mktexfmt [INFO]: /builddir/.texlive2021/texmf-var/web2c/pdftex/latex.fmt installed. mktexfmt [INFO]: successfully rebuilt formats: 1 mktexfmt [INFO]: not selected formats: 19 mktexfmt [INFO]: total formats: 20 mktexfmt [INFO]: exiting with status 0 dec.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating images for formulas in HTML... Generating image form_0.png for formula Generating image form_1.png for formula Generating image form_2.png for formula Generating image form_3.png for formula Generating image form_4.png for formula Generating image form_5.png for formula Generating image form_6.png for formula Generating image form_7.png for formula Generating image form_8.png for formula Generating image form_9.png for formula Generating image form_10.png for formula Generating image form_11.png for formula Generating image form_12.png for formula Generating image form_13.png for formula Generating image form_14.png for formula Generating image form_15.png for formula Generating image form_16.png for formula Generating image form_17.png for formula Generating image form_18.png for formula Generating image form_19.png for formula Generating image form_20.png for formula Generating image form_21.png for formula Generating image form_22.png for formula Generating image form_23.png for formula Generating image form_24.png for formula Generating image form_25.png for formula Generating image form_26.png for formula Generating image form_27.png for formula Generating image form_28.png for formula Generating image form_29.png for formula Generating image form_30.png for formula Generating image form_31.png for formula Generating image form_32.png for formula Generating image form_33.png for formula Generating image form_34.png for formula Generating image form_35.png for formula Generating image form_36.png for formula Generating image form_37.png for formula Generating image form_38.png for formula Generating image form_39.png for formula Generating image form_40.png for formula Generating image form_41.png for formula Generating image form_42.png for formula Generating image form_43.png for formula Generating image form_44.png for formula Generating image form_45.png for formula Generating image form_46.png for formula Generating image form_47.png for formula Generating image form_48.png for formula Generating image form_49.png for formula Generating image form_50.png for formula Generating image form_51.png for formula Generating image form_52.png for formula Generating image form_53.png for formula Generating image form_54.png for formula Generating image form_55.png for formula Generating image form_56.png for formula Generating image form_57.png for formula Generating image form_58.png for formula Generating image form_59.png for formula Generating image form_60.png for formula Generating image form_61.png for formula Generating image form_62.png for formula Generating image form_63.png for formula Generating image form_64.png for formula Generating example documentation... Generating file sources... Generating code for file doc/programmer/mainpage.h... Generating code for file src/apbs.h... Generating code for file src/fem/vcsm.c... Generating code for file src/fem/vcsm.h... Generating code for file src/fem/vfetk.c... Generating code for file src/fem/vfetk.h... Generating code for file src/fem/vpee.c... Generating code for file src/fem/vpee.h... Generating code for file src/generic/apolparm.c... Generating code for file src/generic/apolparm.h... Generating code for file src/generic/bemparm.c... Generating code for file src/generic/bemparm.h... Generating code for file src/generic/femparm.c... Generating code for file src/generic/femparm.h... Generating code for file src/generic/geoflowparm.c... Generating code for file src/generic/geoflowparm.h... Generating code for file src/generic/mgparm.c... Generating code for file src/generic/mgparm.h... Generating code for file src/generic/nosh.c... Generating code for file src/generic/nosh.h... Generating code for file src/generic/pbamparm.c... Generating code for file src/generic/pbamparm.h... Generating code for file src/generic/pbeparm.c... Generating code for file src/generic/pbeparm.h... Generating code for file src/generic/pbsamparm.c... Generating code for file src/generic/pbsamparm.h... Generating code for file src/generic/vacc.c... Generating code for file src/generic/vacc.h... Generating code for file src/generic/valist.c... Generating code for file src/generic/valist.h... Generating code for file src/generic/vatom.c... Generating code for file src/generic/vatom.h... Generating code for file src/generic/vcap.c... Generating code for file src/generic/vcap.h... Generating code for file src/generic/vclist.c... Generating code for file src/generic/vclist.h... Generating code for file src/generic/vgreen.c... Generating code for file src/generic/vgreen.h... Generating code for file src/generic/vhal.h... Generating code for file src/generic/vmatrix.h... Generating code for file src/generic/vparam.c... Generating code for file src/generic/vparam.h... Generating code for file src/generic/vpbe.c... Gene/builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:2095: warning: Member polyEval(int numP, double p[], double c[][VMAXP], double xv[]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1528: warning: Member Vfetk_PDE_initElement(PDE *thee, int elementType, int chart, double tvx[][3], void *data) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1571: warning: Member Vfetk_PDE_initPoint(PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1741: warning: Member Vfetk_PDE_DFu_wv(PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1902: warning: Member Vfetk_PDE_bisectEdge(int dim, int dimII, int edgeType, int chart[], double vx[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1912: warning: Member Vfetk_PDE_mapBoundary(int dim, int dimII, int vertexType, int chart, double vx[3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1917: warning: Member Vfetk_PDE_markSimplex(int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1998: warning: Member Vfetk_PDE_oneChart(int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:86: warning: Member var (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:93: warning: Member diriCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:130: warning: Member neumCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:366: warning: Member dim_2DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:386: warning: Member lgr_2DP1[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:395: warning: Member lgr_2DP1x[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:402: warning: Member lgr_2DP1y[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:409: warning: Member lgr_2DP1z[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:437: warning: Member dim_3DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:438: warning: Member lgr_3DP1[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:446: warning: Member lgr_3DP1x[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:454: warning: Member lgr_3DP1y[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:462: warning: Member lgr_3DP1z[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:476: warning: Member P_DEG (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:482: warning: Member numP (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:483: warning: Member c[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:484: warning: Member cx[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:485: warning: Member cy[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:486: warning: Member cz[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:498: warning: Member Vpee_userDefined(Vpee *thee, SS *sm) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:532: warning: Member Vpee_ourSimp(Vpee *thee, SS *sm, int rcol) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:66: warning: Member Aprx_estNonlinResid(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:72: warning: Member Aprx_estLocalProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:77: warning: Member Aprx_estDualProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:237: warning: Member APOLparm_parseGRID(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:268: warning: Member APOLparm_parseMOL(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:287: warning: Member APOLparm_parseSRFM(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:309: warning: Member APOLparm_parseSRAD(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:328: warning: Member APOLparm_parseSWIN(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:347: warning: Member APOLparm_parseTEMP(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:366: warning: Member APOLparm_parseGAMMA(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:385: warning: Member APOLparm_parseCALCENERGY(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:438: warning: Member APOLparm_parseCALCFORCE(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:491: warning: Member APOLparm_parseBCONC(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:510: warning: Member APOLparm_parseSDENS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:529: warning: Member APOLparm_parseDPOS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:558: warning: Member APOLparm_parsePRESS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:210: warning: Member BEMparm_parseTREE_ORDER(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:233: warning: Member BEMparm_parseTREE_N0(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:256: warning: Member BEMparm_parseMAC(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:279: warning: Member BEMparm_parseMESH(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:308: warning: Member BEMparm_parseOUTDATA(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:196: warning: Member FEMparm_parseDOMAINLENGTH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:221: warning: Member FEMparm_parseETOL(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:244: warning: Member FEMparm_parseEKEY(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:276: warning: Member FEMparm_parseAKEYPRE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:303: warning: Member FEMparm_parseAKEYSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:333: warning: Member FEMparm_parseTARGETNUM(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:352: warning: Member FEMparm_parseTARGETRES(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:372: warning: Member FEMparm_parseMAXSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:391: warning: Member FEMparm_parseMAXVERT(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:411: warning: Member FEMparm_parseUSEMESH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:138: warning: Member FUBAR(const char *name) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:143: warning: Member parseNonNeg(double *tf, double def, int *set, char *name, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:164: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:186: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:415: warning: Member MGparm_parseDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:446: warning: Member MGparm_parseCHGM(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:497: warning: Member MGparm_parseNLEV(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:516: warning: Member MGparm_parseETOL(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:539: warning: Member MGparm_parseGRID(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:570: warning: Member MGparm_parseGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:601: warning: Member MGparm_parseGAMMA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:616: warning: Member MGparm_parseGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:668: warning: Member MGparm_parseCGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:699: warning: Member MGparm_parseFGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:730: warning: Member MGparm_parseCGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:782: warning: Member MGparm_parseFGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:834: warning: Member MGparm_parsePDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:872: warning: Member MGparm_parseOFRAC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:892: warning: Member MGparm_parseASYNC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:912: warning: Member MGparm_parseUSEAQUA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:970: warning: Member NOsh_parseREAD(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1021: warning: Member NOsh_parsePRINT(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1187: warning: Member NOsh_parseELEC(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1313: warning: Member NOsh_parseAPOLAR(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2385: warning: Member NOsh_parseFEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1510: warning: Member NOsh_parseMG(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2845: warning: Member NOsh_parseBEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2934: warning: Member NOsh_parseGEOFLOW(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3048: warning: Member NOsh_parsePBAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3166: warning: Member NOsh_parsePBSAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2508: warning: Member NOsh_parseAPOL(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1603: warning: Member NOsh_setupCalcMG(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1815: warning: Member NOsh_setupCalcMGAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1747: warning: Member NOsh_setupCalcMGMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2090: warning: Member NOsh_setupCalcMGPARA(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1722: warning: Member NOsh_setupCalcFEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2471: warning: Member NOsh_setupCalcFEMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1638: warning: Member NOsh_setupCalcBEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1666: warning: Member NOsh_setupCalcGEOFLOW(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1686: warning: Member NOsh_setupCalcPBAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1704: warning: Member NOsh_setupCalcPBSAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2612: warning: Member NOsh_setupCalcBEMMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2677: warning: Member NOsh_setupCalcGEOFLOWMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2735: warning: Member NOsh_setupCalcPBAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2786: warning: Member NOsh_setupCalcPBSAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2581: warning: Member NOsh_setupCalcAPOL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:598: warning: Member NOsh_parseREAD_MOL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:675: warning: Member NOsh_parseREAD_PARM(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:739: warning: Member NOsh_parseREAD_DIEL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:793: warning: Member NOsh_parseREAD_KAPPA(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:839: warning: Member NOsh_parseREAD_POTENTIAL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:884: warning: Member NOsh_parseREAD_CHARGE(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:930: warning: Member NOsh_parseREAD_MESH(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:458: warning: Member PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:549: warning: Member PBAMparm_parseTerm(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:77: warning: Member PBAMPARM_MAXWRITE (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:78: warning: Member PBAMPARM_MAXMOL (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:87: warning: Member PBEparm_getzmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:91: warning: Member PBEparm_getLmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:95: warning: Member PBEparm_getmembraneDiel(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:99: warning: Member PBEparm_getmemv(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:368: warning: Member PBEparm_parseLPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:375: warning: Member PBEparm_parseNPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:382: warning: Member PBEparm_parseMOL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:401: warning: Member PBEparm_parseLRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:408: warning: Member PBEparm_parseNRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:415: warning: Member PBEparm_parseSMPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:474: warning: Member PBEparm_parseBCFL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:555: warning: Member PBEparm_parseION(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:652: warning: Member PBEparm_parsePDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:671: warning: Member PBEparm_parseSDENS(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:690: warning: Member PBEparm_parseSDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:709: warning: Member PBEparm_parseSRFM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:780: warning: Member PBEparm_parseSRAD(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:799: warning: Member PBEparm_parseSWIN(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:818: warning: Member PBEparm_parseTEMP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:837: warning: Member PBEparm_parseUSEMAP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:895: warning: Member PBEparm_parseCALCENERGY(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:948: warning: Member PBEparm_parseCALCFORCE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1005: warning: Member PBEparm_parseZMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1025: warning: Member PBEparm_parseLMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1044: warning: Member PBEparm_parseMDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1063: warning: Member PBEparm_parseMEMV(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1084: warning: Member PBEparm_parseWRITE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1178: warning: Member PBEparm_parseWRITEMAT(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:77: warning: Member PBSAMPARM_MAXWRITE (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:78: warning: Member PBSAMPARM_MAXMOL (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:277: warning: Member Vacc_vdwAcc(Vacc *thee, double center[3]) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:307: warning: Member Vacc_ivdwAcc(Vacc *thee, double center[3], double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:679: warning: Member Vacc_writeGMV(Vacc *thee, double radius, int meth, Gem *gm, char *iodev, char *iofmt, char *iohost, char *iofile) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1252: warning: Member Vacc_SASAPos(Vacc *thee, double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1277: warning: Member Vacc_atomSASAPos(Vacc *thee, double radius, Vatom *atom, int mode) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:76: warning: The following parameter of ivdwAccExclus(Vacc *thee, double center[3], double radius, int atomID) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:490: warning: The following parameter of splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:186: warning: Member Valist_readPDBSerial(Valist *thee, Vio *sock, int *serial) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:206: warning: Member Valist_readPDBAtomName(Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:224: warning: Member Valist_readPDBResidueName(Valist *thee, Vio *sock, char resName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:242: warning: Member Valist_readPDBResidueNumber(Valist *thee, Vio *sock, int *resSeq) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:298: warning: Member Valist_readPDBAtomCoord(Valist *thee, Vio *sock, double *coord) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:316: warning: Member Valist_readPDBChargeRadius(Valist *thee, Vio *sock, double *charge, double *radius) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:344: warning: Member Valist_readPDB_throughXYZ(Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:424: warning: Member Valist_getAtomStorage(Valist *thee, Vatom **plist, int *pnlist, int *pnatoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:480: warning: Member Valist_setAtomArray(Valist *thee, Vatom **plist, int nlist, int natoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:60: warning: Member Valist_whiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:61: warning: Member Valist_commChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:62: warning: Member Valist_xmlwhiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:128: warning: Member VCLIST_INFLATE (macro definition) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:90: warning: Member Vclist_getMolDims(Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:125: warning: Member Vclist_setupGrid(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:174: warning: Member Vclist_storeParms(Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:231: warning: Member Vclist_gridSpan(Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:262: warning: Member Vclist_arrayIndex(Vclist *thee, int i, int j, int k) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:270: warning: Member Vclist_assignAtoms(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425: warning: Member treesetup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505: warning: Member treecleanup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525: warning: Member treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, double *qtar, int numtars, double *tpengtar, double *x, double *y, double *z, double *q, int numpars, double *fx, double *fy, double *fz, int iflag, int farrdim, int arrdim) (function) of file vgreen.c is not documented. rating code for file src/generic/vpbe.h... Generating code for file src/generic/vstring.c... Generating code for file src/generic/vstring.h... Generating code for file src/generic/vunit.h... Generating code for file src/main.c... Generating code for file src/mg/vgrid.c... Generating code for file src/mg/vgrid.h... Generating code for file src/mg/vmgrid.c... Generating code for file src/mg/vmgrid.h... Generating code for file src/mg/vopot.c... Generating code for file src/mg/vopot.h... Generating code for file src/mg/vpmg.c... Generating code for file src/mg/vpmg.h... Generating code for file src/mg/vpmgp.c... Generating code for file src/mg/vpmgp.h... Generating code for file src/pmgc/buildAd.c... Generating code for file src/pmgc/buildAd.h... Generating code for file src/pmgc/buildBd.c... Generating code for file src/pmgc/buildBd.h... Generating code for file src/pmgc/buildGd.c... Generating code for file src/pmgc/buildGd.h... Generating code for file src/pmgc/buildPd.c... Generating code for file src/pmgc/buildPd.h... Generating code for file src/pmgc/cgd.c... Generating code for file src/pmgc/cgd.h... Generating code for file src/pmgc/gsd.c... Generating code for file src/pmgc/gsd.h... Generating code for file src/pmgc/matvecd.c... Generating code for file src/pmgc/matvecd.h... Generating code for file src/pmgc/mgcsd.c... Generating code for file src/pmgc/mgcsd.h... Generating code for file src/pmgc/mgdrvd.c... Generating code for file src/pmgc/mgdrvd.h... Generating code for file src/pmgc/mgfasd.c... Generating code for file src/pmgc/mgfasd.h... Generating code for file src/pmgc/mgsubd.c... Generating code for file src/pmgc/mgsubd.h... Generating code for file src/pmgc/mikpckd.c... Generating code for file src/pmgc/mikpckd.h... Generating code for file src/pmgc/mlinpckd.c... Generating code for file src/pmgc/mlinpckd.h... Generating code for file src/pmgc/mypdec.c... Generating code for file src/pmgc/mypdec.h... Generating code for file src/pmgc/newdrvd.c... Generating code for file src/pmgc/newdrvd.h... Generating code for file src/pmgc/newtond.c... Generating code for file src/pmgc/newtond.h... Generating code for file src/pmgc/powerd.c... Generating code for file src/pmgc/powerd.h... Generating code for file src/pmgc/smoothd.c... Generating code for file src/pmgc/smoothd.h... Generating code for file src/routines.c... Generating code for file src/routines.h... Generating file documentation... Generating docs for file src/apbs.h... Generating docs for file src/fem/vcsm.c... Generating docs for file src/fem/vcsm.h... Generating docs for file src/fem/vfetk.c... Generating docs for file src/fem/vfetk.h... Generating docs for file src/fem/vpee.c... Generating docs for file src/fem/vpee.h... Generating docs for file src/generic/apolparm.c... Generating docs for file src/generic/bemparm.c... Generating docs for file src/generic/femparm.c... Generating docs for file src/generic/femparm.h... Generating docs for file src/generic/geoflowparm.c... Generating docs for file src/generic/geoflowparm.h... Generating docs for file src/generic/mgparm.c... Generating docs for file src/generic/mgparm.h... Generating docs for file src/generic/nosh.c... Generating docs for file src/generic/nosh.h... Generating docs for file src/generic/pbamparm.c... Generating docs for file src/generic/pbamparm.h... Generating docs for file src/generic/pbeparm.c... Generating docs for file src/generic/pbeparm.h... Generating docs for file src/generic/pbsamparm.c... Generating docs for file src/generic/pbsamparm.h... Generating docs for file src/generic/vacc.c... Generating docs for file src/generic/vacc.h... Generating docs for file src/generic/valist.c... Generating docs for file src/generic/valist.h... Generating docs for file src/generic/vatom.c... Generating docs for file src/generic/vatom.h... Generating docs for file src/generic/vcap.c... Generating docs for file src/generic/vcap.h... Generating docs for file src/generic/vclist.c... Generating docs for file src/generic/vclist.h... Generating docs for file src/generic/vgreen.c... Generating docs fo/builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:458: warning: Member MAX_HASH_DIM (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:572: warning: Member OS_SEP_STR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:573: warning: Member OS_SEP_CHAR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:600: warning: Member ANNOUNCE_FUNCTION (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:601: warning: Member WARN_UNTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:602: warning: Member WARN_PARTTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:653: warning: Member VCHANNELEDMESSAGE0(channel, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:658: warning: Member VCHANNELEDMESSAGE1(channel, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:665: warning: Member VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:672: warning: Member VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:679: warning: Member VMESSAGE0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:680: warning: Member VMESSAGE1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:681: warning: Member VMESSAGE2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:682: warning: Member VMESSAGE3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:684: warning: Member VERRMSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:685: warning: Member VERRMSG1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:686: warning: Member VERRMSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:687: warning: Member VERRMSG3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:731: warning: Member VASSERT_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:741: warning: Member VASSERT_MSG1(cnd, msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:753: warning: Member VASSERT_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:825: warning: Member VWARN_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:838: warning: Member VWARN_MSG1(cnd, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:853: warning: Member VWARN_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:899: warning: Member VABORT_MSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:907: warning: Member VABORT_MSG1(msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:917: warning: Member VABORT_MSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:944: warning: Member PRINT_INT(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:945: warning: Member PRINT_DBL(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:948: warning: Member VMALLOC(vmem, n, type) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:950: warning: Member VFREE(vmem, n, type, ptr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:952: warning: Member VFILL(vec, n, val) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:959: warning: Member VCOPY(srcvec, dstvec, i, n) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:968: warning: Member VAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:969: warning: Member RAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:73: warning: Member Vrc_Codes (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:95: warning: Member Vsol_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:966: warning: Member wrap_text(char *str, int right_margin, int left_padding) (function) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:64: warning: Member MAT2(mat, dx, dy) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:68: warning: Member RAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:71: warning: Member VAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:76: warning: Member MAT3(mat, dx, dy, dz) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:81: warning: Member RAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:84: warning: Member VAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c:62: warning: Member MAX_SPLINE_WINDOW (macro definition) of file vpbe.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:67: warning: Member IJK(i, j, k) (macro definition) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:77: warning: Member MCwhiteChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:78: warning: Member MCcommChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:79: warning: Member Vcompare (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:80: warning: Member Vprecision[26] (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:113: warning: Member IJK(i, j, k) (macro definition) of file vopot.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1401: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828: warning: Member bcCalcOrig(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3130: warning: Member gridPointIsValid(int i, int j, int k, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3313: warning: Member packAtoms(double *ax, double *ay, double *az, double *charge, double *size, Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3338: warning: Member packUnpack(int nx, int ny, int nz, int ngrid, double *gx, double *gy, double *gz, double *value, Vpmg *thee, int pack) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3407: warning: Member bcflnew(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3597: warning: Member bcfl_sdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868: warning: Member bcfl_mdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3995: warning: Member bcfl_mem(double zmem, double L, double eps_m, double eps_w, double V, double xkappa, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4174: warning: Member bcfl_map(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684: warning: Member markFrac(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *xarray, double *yarray, double *zarray) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10260: warning: Member fillcoPermanentInduced(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: argument 'hz' of command @param is not found in the argument list of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1107: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:105: warning: Member VPMGMAXPART (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1392: warning: Member VCUB(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1393: warning: Member VLOG(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1395: warning: Member IJK(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1396: warning: Member IJKx(j, k, i) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1397: warning: Member IJKy(i, k, j) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1398: warning: Member IJKz(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1399: warning: Member VFCHI(iint, iflt) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1107: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:294: warning: Member coarsenThis(int nOld) (function) of file vpmgp.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: argument 'parm' of command @param is not found in the argument list of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: The following parameter of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) is not documented: parameter 'sock' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:513: warning: The following parameter of energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) is not documented: parameter 'apolparm' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:610: warning: The following parameter of killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:262: warning: The following parameter of killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: argument 'charge' of command @param is not found in the argument list of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: The following parameter of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: argument 'kappa' of command @param is not found in the argument list of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: The following parameter of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: argument 'pot' of command @param is not found in the argument list of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: The following parameter of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:622: warning: argument 'nosh' of command @param is not found in the argument list of preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/routines.h:494: warning: The following parameter of printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:445: warning: The following parameter of printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:481: warning: The following parameter of printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:432: warning: The following parameter of printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:468: warning: The following parameter of printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4125: warning: argument 'i' of command @param is not found in the argument list of solveFE(int icalc, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:104: warning: Member vdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:105: warning: Member setvdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:111: warning: Member salt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:112: warning: Member setsalt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:115: warning: Member runtype[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:116: warning: Member setruntype (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:119: warning: Member runname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:120: warning: Member setrunname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:123: warning: Member setrandorient (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:126: warning: Member pbcboxlen (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:127: warning: Member setpbcs (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:130: warning: Member units[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:131: warning: Member setunits (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:137: warning: Member gridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:138: warning: Member setgridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:141: warning: Member map3dname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:142: warning: Member set3dmap (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:145: warning: Member grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:146: warning: Member grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:147: warning: Member grid2Dloc[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:148: warning: Member grid2Dct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:149: warning: Member setgrid2Dname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:152: warning: Member dxname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:153: warning: Member setdxname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:158: warning: Member ntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:159: warning: Member setntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:161: warning: Member termcombine[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:162: warning: Member settermcombine (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:164: warning: Member diffct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:165: warning: Member moveType[PBAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:166: warning: Member transDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:167: warning: Member rotDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:169: warning: Member termct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:170: warning: Member setterm (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:172: warning: Member termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:173: warning: Member termnu[PBAMPARM_MAXWRITE][1] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:174: warning: Member termVal[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:175: warning: Member confil[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:176: warning: Member conpad[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:177: warning: Member confilct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:179: warning: Member setxyz (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:180: warning: Member xyzct[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:181: warning: Member xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:202: warning: Member pbam_3dmapstem[VMAX_ARGLEN] (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:203: warning: Member pbam_3dmapflag (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:112: warning: Member settolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:113: warning: Member tolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:115: warning: Member setmsms (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:116: warning: Member probe_radius (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:117: warning: Member density (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:119: warning: Member setsurf (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:120: warning: Member surfct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:121: warning: Member surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:123: warning: Member setimat (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:124: warning: Member imatct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:125: warning: Member imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:127: warning: Member setexp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:128: warning: Member expct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:129: warning: Member expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. r file src/generic/vgreen.h... Generating docs for file src/generic/vhal.h... Generating docs for file src/generic/vmatrix.h... Generating docs for file src/generic/vparam.c... Generating docs for file src/generic/vparam.h... Generating docs for file src/generic/vpbe.c... Generating docs for file src/generic/vpbe.h... Generating docs for file src/generic/vstring.c... Generating docs for file src/generic/vstring.h... Generating docs for file src/generic/vunit.h... Generating docs for file src/main.c... Generating docs for file src/mg/vgrid.c... Generating docs for file src/mg/vgrid.h... Generating docs for file src/mg/vmgrid.c... Generating docs for file src/mg/vmgrid.h... Generating docs for file src/mg/vopot.c... Generating docs for file src/mg/vopot.h... Generating docs for file src/mg/vpmg.c... Generating docs for file src/mg/vpmg.h... Generating docs for file src/mg/vpmgp.c... Generating docs for file src/mg/vpmgp.h... Generating docs for file src/routines.c... Generating docs for file src/routines.h... Generating page documentation... Generating docs for page bug... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound AtomForce... Generating docs for compound sAPOLparm... Generating docs for compound sBEMparm... Generating docs for compound sFEMparm... Generating docs for compound sGEOFLOWparm... Generating docs for compound sMGparm... Generating docs for compound sNOsh... Generating docs for compound sNOsh_calc... Generating docs for compound sPBAMparm... Generating docs for compound sPBEparm... Generating docs for compound sPBSAMparm... Generating docs for compound sVacc... Generating docs for compound sVaccSurf... Generating docs for compound sValist... Generating docs for compound sVatom... Generating docs for compound sVclist... Generating docs for compound sVclistCell... Generating docs for compound sVcsm... Generating docs for compound sVfetk... Generating docs for compound sVfetk_LocalVar... Generating docs for compound sVgreen... Generating docs for compound sVgrid... Generating docs for compound sVmgrid... Generating docs for compound sVopot... Generating docs for compound sVparam_AtomData... Generating docs for compound sVpbe... Generating docs for compound sVpee... Generating docs for compound sVpmg... Generating docs for compound sVpmgp... Generating docs for compound Vparam... Generating docs for compound Vparam_ResData... Generating concept documentation... Generating namespace index... Generating graph info page... Generating directory documentation... Generating dependency graph for directory src/fem Generating dependency graph for directory src/generic Generating dependency graph for directory src/mg Generating dependency graph for directory src/pmgc Generating dependency graph for directory doc/programmer Generating dependency graph for directory src Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 6 parallel threads... Running dot for graph 1/175 Running dot for graph 2/175 Running dot for graph 3/175 Running dot for graph 4/175 Running dot for graph 5/175 Running dot for graph 6/175 Running dot for graph 7/175 Running dot for graph 8/175 Running dot for graph 9/175 Running dot for graph 10/175 Running dot for graph 11/175 Running dot for graph 12/175 Running dot for graph 13/175 Running dot for graph 14/175 Running dot for graph 15/175 Running dot for graph 16/175 Running dot for graph 17/175 Running dot for graph 18/175 Running dot for graph 19/175 Running dot for graph 20/175 Running dot for graph 21/175 Runerror: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.pdf error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.pdf"' /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.pdf"' ning dot for graph 22/175 Running dot for graph 23/175 Running dot for graph 24/175 Running dot for graph 25/175 Running dot for graph 26/175 Running dot for graph 27/175 Running dot for graph 28/175 Running dot for graph 29/175 Running dot for graph 30/175 Running dot for graph 31/175 Running dot for graph 32/175 Running dot for graph 33/175 Running dot for graph 34/175 Running dot for graph 35/175 Running dot for graph 36/175 Running dot for graph 37/175 Running dot for graph 38/175 Running dot for graph 39/175 Running dot for graph 40/175 Running dot for graph 41/175 Running dot for graph 42/175 Running dot for graph 43/175 Running dot for graph 44/175 Running dot for graph 45/175 Running dot for graph 46/175 Running dot for graph 47/175 Running dot for graph 48/175 Running dot for graph 49/175 Running dot for graph 50/175 Running dot for graph 51/175 Running dot for graph 52/175 Running dot for graph 53/175 Running dot for graph 54/175 Running dot for graph 55/175 Running dot for graph 56/175 Running dot for graph 57/175 Running dot for graph 58/175 Running dot for graph 59/175 Running dot for graph 60/175 Running dot for graph 61/175 Running dot for graph 62/175 Running dot for graph 63/175 Running dot for graph 64/175 Running dot for graph 65/175 Running dot for graph 66/175 Running dot for graph 67/175 Running dot for graph 68/175 Running dot for graph 69/175 Running dot for graph 70/175 Running dot for graph 71/175 Running dot for graph 72/175 Running dot for graph 73/175 Running dot for graph 74/175 Running dot for graph 75/175 Running dot for graph 76/175 Running dot for graph 77/175 Running dot for graph 78/175 Running dot for graph 79/175 Running dot for graph 80/175 Running dot for graph 81/175 Running dot for graph 82/175 Running dot for graph 83/175 Running dot for graph 84/175 Running dot for graph 85/175 Running dot for graph 86/175 Running dot for graph 87/175 Running dot for graph 88/175 Running dot for graph 89/175 Running dot for graph 90/175 Running dot for graph 91/175 Running dot for graph 92/175 Running dot for graph 93/175 Running dot for graph 94/175 Running dot for graph 95/175 Running dot for graph 96/175 Running dot for graph 97/175 Running dot for graph 98/175 Running dot for graph 99/175 Running dot for graph 100/175 Running dot for graph 101/175 Running dot for graph 102/175 Running dot for graph 103/175 Running dot for graph 104/175 Running dot for graph 105/175 Running dot for graph 106/175 Running dot for graph 107/175 Running dot for graph 108/175 Running dot for graph 109/175 Running dot for graph 110/175 Running dot for graph 111/175 Running dot for graph 112/175 Running dot for graph 113/175 Running dot for graph 114/175 Running dot for graph 115/175 Running dot for graph 116/175 Running dot for graph 117/175 Running dot for graph 118/175 Running dot for graph 119/175 Running dot for graph 120/175 Running dot for graph 121/175 Running dot for graph 122/175 Running dot for graph 123/175 Running dot for graph 124/175 Running dot for graph 125/175 Running dot for graph 126/175 Running dot for graph 127/175 Running dot for graph 128/175 Running dot for graph 129/175 Running dot for graph 130/175 Running dot for graph 131/175 Running dot for graph 132/175 Running dot for graph 133/175 Running dot for graph 134/175 Running dot for graph 135/175 Running dot for graph 136/175 Running dot for graph 137/175 Running dot for graph 138/175 Running dot for graph 139/175 Running dot for graph 140/175 Running dot for graph 141/175 Running dot for graph 142/175 Running dot for graph 143/175 Running dot for graph 144/175 Running dot for graph 145/175 Running dot for graph 146/175 Running dot for graph 147/175 Running dot for graph 148/175 Running dot for graph 149/175 Running dot for graph 150/175 Running dot for graph 151/175 Running dot for graph 152/175 Running dot for graph 153/175 Running dot for graph 154/175 Running dot for graph 155/175 Running dot for graph 156/175 Running dot for graph 157/175 Running dot for graph 158/175 Running dot for graph 159/175 Running dot for graph 160/175 Runningerror: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.pdf error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.pdf"' /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf error: problem writing FIG 0 figure! dot for graph 161/175 Running dot for graph 162/175 Running dot for graph 163/175 Running dot for graph 164/175 Running dot for graph 165/175 Running dot for graph 166/175 Running dot for graph 167/175 Running dot for graph 168/175 Running dot for graph 169/175 Running dot for graph 170/175 Running dot for graph 171/175 Running dot for graph 172/175 Running dot for graph 173/175 Running dot for graph 174/175 Running dot for graph 175/175 Patching output file 1/120 Patching output file 2/120 Patching output file 3/120 Patching output file 4/120 Patching output file 5/120 Patching output file 6/120 Patching output file 7/120 Patching output file 8/120 Patching output file 9/120 Patching output file 10/120 Patching output file 11/120 Patching output file 12/120 Patching output file 13/120 Patching output file 14/120 Patching output file 15/120 Patching output file 16/120 Patching output file 17/120 Patching output file 18/120 Patching output file 19/120 Patching output file 20/120 Patching output file 21/120 Patching output file 22/120 Patching output file 23/120 Patching output file 24/120 Patching output file 25/120 Patching output file 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output file 62/120 Patching output file 63/120 Patching output file 64/120 lookup cache used 2285/65536 hits=43969 misses=2419 finished... make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Built target doc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 55%] Generating pdf documentation make[3]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/latex' This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex) restricted \write18 enabled. kpathsea: Running mktexfmt pdflatex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.texlive2021/texmf-config/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.texlive2021/texmf-var/web2c mktexfmt [INFO]: --- remaking pdflatex with pdftex mktexfmt: running `pdftex -ini -jobname=pdflatex -progname=pdflatex -translate-file=cp227.tcx *pdflatex.ini' ... This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (INITEX) restricted \write18 enabled. (/usr/share/texlive/texmf-dist/web2c/cp227.tcx) entering extended mode (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/pdflatex.ini (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex) (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. Defining UNIX/DOS style filename parser. catcodes, registers, parameters, LaTeX2e <2020-10-01> patch level 4 (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.ltx (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3-code.tex (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/l3deprecation.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.ltx (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse-generic.tex)) hacks, control, par, spacing, files, font encodings, lengths, ==================================== Local config file fonttext.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmss.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmtt.fd))) ==================================== Local config file fontmath.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmm.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmsy.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omxcmex.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ucmr.fd))) ==================================== Local config file preload.cfg used ===================================== (/usr/share/texlive/texmf-dist/tex/latex/base/preload.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/preload.ltx)) page nos., x-ref, environments, center, verbatim, math definitions, boxes, title, sectioning, contents, floats, footnotes, index, bibliography, output, =========================================== Local configuration file hyphen.cfg used =========================================== (/usr/share/texlive/texmf-dist/tex/generic/babel/hyphen.cfg (/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/dumyhyph.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/zerohyph.tex)) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/share/texlive/texmf-dist/tex/latex/firstaid/latex2e-first-aid-for-externa l-files.ltx) ) ) Beginning to dump on file pdflatex.fmt (preloaded format=pdflatex 2022.7.20) 19194 strings of total length 344849 280641 memory locations dumped; current usage is 165&279285 17486 multiletter control sequences \font\nullfont=nullfont \font\c__fp_exp_intarray=cmr10 at 0.00002pt \font\c__fp_trig_intarray=cmr10 at 0.00003pt \font\c_initex_cctab=cmr10 at 0.00005pt \font\c_other_cctab=cmr10 at 0.00006pt \font\c_str_cctab=cmr10 at 0.00008pt \font\g__regex_state_active_intarray=cmr10 at 0.00009pt \font\g__regex_thread_info_intarray=cmr10 at 0.0001pt \font\g__regex_submatch_prev_intarray=cmr10 at 0.00012pt \font\g__regex_submatch_begin_intarray=cmr10 at 0.00014pt \font\g__regex_submatch_end_intarray=cmr10 at 0.00015pt \font\g__regex_balance_intarray=cmr10 at 0.00017pt \font\OMX/cmex/m/n/10=cmex10 \font\tenln=line10 \font\tenlnw=linew10 \font\tencirc=lcircle10 \font\tencircw=lcirclew10 \font\OT1/cmr/m/n/5=cmr5 \font\OT1/cmr/m/n/7=cmr7 \font\OT1/cmr/m/n/10=cmr10 \font\OML/cmm/m/it/5=cmmi5 \font\OML/cmm/m/it/7=cmmi7 \font\OML/cmm/m/it/10=cmmi10 \font\OMS/cmsy/m/n/5=cmsy5 \font\OMS/cmsy/m/n/7=cmsy7 \font\OMS/cmsy/m/n/10=cmsy10 \font\c_code_cctab=cmr10 at 0.00018pt \font\c_document_cctab=cmr10 at 0.0002pt 403423 words of font info for 27 preloaded fonts 14 hyphenation exceptions Hyphenation trie of length 6081 has 183 ops out of 35111 2 for language 1 181 for language 0 0 words of pdfTeX memory 0 indirect objects No pages of output. Transcript written on pdflatex.log. mktexfmt [INFO]: log file copied to: /builddir/.texlive2021/texmf-var/web2c/pdftex/pdflatex.log mktexfmt [INFO]: /builddir/.texlive2021/texmf-var/web2c/pdftex/pdflatex.fmt installed. mktexfmt [INFO]: successfully rebuilt formats: 1 mktexfmt [INFO]: not selected formats: 19 mktexfmt [INFO]: total formats: 20 mktexfmt [INFO]: exiting with status 0 entering extended mode (./refman.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-05-07> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array-2016-10-06.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) All fixes are now in the LaTeX kernel. 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LaTeX Warning: Reference `smoothd_8h_source' on page 18 undefined on input line 98. ) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.1 on input line 102. Overfull \vbox (13.81569pt too high) has occurred while \output is active [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.2 on input line 130. Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.3 on input line 164. 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[38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.32 on input line 805. Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.33 on input line 835. Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Package longtable Warning: Column widths have changed (longtable) in table 7.34 on input line 860. 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[47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.52 on input line 1376. Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Package longtable Warning: Column widths have changed (longtable) in table 7.53 on input line 1412. Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.54 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.55 on input line 1472. 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[60] Underfull \hbox (badness 10000) detected at line 171 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.72 on input line 178. Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.73 on input line 226. [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.74 on input line 251. ) (./group___a_p_o_lparm.tex [62] [63] Package longtable Warning: Column widths have changed (longtable) in table 7.75 on input line 154. Package longtable Warning: Column widths have changed (longtable) in table 7.76 on input line 182. 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Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.119 on input line 481. Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.120 on input line 506. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.121 on input line 531. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.122 on input line 556. Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.123 on input line 581. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.124 on input line 606. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.125 on input line 631. [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.126 on input line 660. Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.127 on input line 687. [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.128 on input line 711. Underfull \hbox (badness 10000) detected at line 726 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.129 on input line 735. ) (./group___n_osh.tex [91] [92] [93] [94] Package longtable Warning: Column widths have changed (longtable) in table 7.130 on input line 337. [95] Package longtable Warning: Column widths have changed (longtable) in table 7.131 on input line 365. Package longtable Warning: Column widths have changed (longtable) in table 7.132 on input line 389. Package longtable Warning: Column widths have changed (longtable) in table 7.133 on input line 429. [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.134 on input line 456. Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.135 on input line 483. Underfull \hbox (badness 10000) detected at line 498 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.136 on input line 505. [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.137 on input line 530. Underfull \hbox (badness 10000) detected at line 545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.138 on input line 554. Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.139 on input line 583. Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.140 on input line 608. Underfull \hbox (badness 10000) detected at line 623 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.141 on input line 630. [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.142 on input line 654. Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.143 on input line 684. Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.144 on input line 714. Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.145 on input line 741. Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.146 on input line 768. Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.147 on input line 795. Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.148 on input line 822. Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.149 on input line 849. Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.150 on input line 876. Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Package longtable Warning: Column widths have changed (longtable) in table 7.151 on input line 903. Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.152 on input line 930. Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.153 on input line 957. [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.154 on input line 984. Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.155 on input line 1011. Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.156 on input line 1041. Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.157 on input line 1073. Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.158 on input line 1105. Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.159 on input line 1138. Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.160 on input line 1173. Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Package longtable Warning: Column widths have changed (longtable) in table 7.161 on input line 1206. Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.162 on input line 1239. Underfull \hbox (badness 10000) detected at line 1240 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.163 on input line 1249. [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.164 on input line 1276. Underfull \hbox (badness 10000) detected at line 1277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.165 on input line 1286. ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.166 on input line 154. Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.167 on input line 179. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.168 on input line 206. [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.169 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.170 on input line 255. Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.171 on input line 280. [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.172 on input line 302. Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.173 on input line 326. Underfull \hbox (badness 10000) detected at line 341 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.174 on input line 350. [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.175 on input line 374. Underfull \hbox (badness 10000) detected at line 389 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.176 on input line 398. Underfull \hbox (badness 10000) detected at line 413 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.177 on input line 422. [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.178 on input line 446. Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.179 on input line 470. Underfull \hbox (badness 10000) detected at line 485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.180 on input line 494. Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.181 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.182 on input line 542. Underfull \hbox (badness 10000) detected at line 557 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.183 on input line 566. Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.184 on input line 592. Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.185 on input line 619. [119] Underfull \hbox (badness 10000) detected at line 634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.186 on input line 643. ) (./group___p_b_eparm.tex [120] [121] Package longtable Warning: Column widths have changed (longtable) in table 7.187 on input line 163. Package longtable Warning: Column widths have changed (longtable) in table 7.188 on input line 191. [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.189 on input line 219. Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.190 on input line 243. Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.191 on input line 288. Underfull \hbox (badness 10000) detected at line 303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.192 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.193 on input line 332. [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.194 on input line 359. Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.195 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Package longtable Warning: Column widths have changed (longtable) in table 7.196 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.197 on input line 442. ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.198 on input line 138. [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.199 on input line 163. Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.200 on input line 190. Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.201 on input line 212. Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.202 on input line 239. Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.203 on input line 264. Underfull \hbox (badness 10000) detected at line 279 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.204 on input line 286. [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.205 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.206 on input line 334. Underfull \hbox (badness 10000) detected at line 349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.207 on input line 358. Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.208 on input line 382. Underfull \hbox (badness 10000) detected at line 397 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.209 on input line 408. Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.210 on input line 435. ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.211 on input line 164. Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.212 on input line 192. [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.213 on input line 224. Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.214 on input line 253. [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.215 on input line 282. Underfull \hbox (badness 10000) detected at line 283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.216 on input line 290. Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.217 on input line 319. [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.218 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.219 on input line 372. [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.220 on input line 394. Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.221 on input line 430. [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.222 on input line 461. Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.223 on input line 482. Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.224 on input line 515. Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.225 on input line 545. [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.226 on input line 578. Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.227 on input line 613. [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.228 on input line 643. Underfull \hbox (badness 10000) detected at line 660 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.229 on input line 677. [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.230 on input line 709. Underfull \hbox (badness 10000) detected at line 724 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.231 on input line 741. [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.232 on input line 775. Underfull \hbox (badness 10000) detected at line 790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.233 on input line 805. Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.234 on input line 837. Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.235 on input line 867. [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.236 on input line 901. Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.237 on input line 930. Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.238 on input line 957. Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.239 on input line 992. [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.240 on input line 1025. Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Package longtable Warning: Column widths have changed (longtable) in table 7.241 on input line 1054. Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.242 on input line 1085. Underfull \hbox (badness 10000) detected at line 1100 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.243 on input line 1107. [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.244 on input line 1129. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.245 on input line 1161. ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.246 on input line 121. Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Package longtable Warning: Column widths have changed (longtable) in table 7.247 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.248 on input line 165. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.249 on input line 192. [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.250 on input line 217. Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.251 on input line 242. Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.252 on input line 267. [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.253 on input line 292. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.254 on input line 317. Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.255 on input line 362. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.256 on input line 394. [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.257 on input line 428. Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159] Package longtable Warning: Column widths have changed (longtable) in table 7.258 on input line 462. ) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.259 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.260 on input line 167. [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.261 on input line 209. Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.262 on input line 234. [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.263 on input line 256. Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.264 on input line 278. Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.265 on input line 305. [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.266 on input line 327. Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.267 on input line 352. Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.268 on input line 377. [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.269 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.270 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.271 on input line 454. Underfull \hbox (badness 10000) detected at line 469 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.272 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.273 on input line 503. [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.274 on input line 527. Underfull \hbox (badness 10000) detected at line 542 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.275 on input line 551. Underfull \hbox (badness 10000) detected at line 566 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.276 on input line 575. [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.277 on input line 599. Underfull \hbox (badness 10000) detected at line 614 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.278 on input line 623. Underfull \hbox (badness 10000) detected at line 638 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.279 on input line 647. [169] Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.280 on input line 671. ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.281 on input line 101. Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.282 on input line 134. Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.283 on input line 167. ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.284 on input line 138. Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.285 on input line 176. [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.286 on input line 213. Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Package longtable Warning: Column widths have changed (longtable) in table 7.287 on input line 235. Underfull \hbox (badness 10000) detected at line 250 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.288 on input line 257. Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.289 on input line 284. [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.290 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.291 on input line 334. Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.292 on input line 359. [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.293 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.294 on input line 408. Underfull \hbox (badness 10000) detected at line 423 [][][] [179] Package longtable Warning: Column widths have changed (longtable) in table 7.295 on input line 430. ) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.296 on input line 158. Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.297 on input line 195. Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.298 on input line 238. Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.299 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.300 on input line 306. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Package longtable Warning: Column widths have changed (longtable) in table 7.301 on input line 333. Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.302 on input line 358. Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.303 on input line 380. [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.304 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.305 on input line 448. [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.306 on input line 499. Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.307 on input line 524. Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.308 on input line 794. Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.309 on input line 825. Underfull \hbox (badness 10000) detected at line 840 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.310 on input line 860. Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.311 on input line 907. [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. Package longtable Warning: Column widths have changed (longtable) in table 7.312 on input line 986. [199] Package longtable Warning: Column widths have changed (longtable) in table 7.313 on input line 1014. Package longtable Warning: Column widths have changed (longtable) in table 7.314 on input line 1060. Package longtable Warning: Column widths have changed (longtable) in table 7.315 on input line 1084. Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.316 on input line 1115. Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.317 on input line 1175. ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.318 on input line 161. Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.319 on input line 188. Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.320 on input line 215. [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.321 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.322 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.323 on input line 306. Underfull \hbox (badness 10000) detected at line 321 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.324 on input line 328. Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Package longtable Warning: Column widths have changed (longtable) in table 7.325 on input line 370. Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.326 on input line 395. Underfull \hbox (badness 10000) detected at line 410 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.327 on input line 417. [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.328 on input line 443. Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.329 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.330 on input line 507. Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.331 on input line 540. Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.332 on input line 584. Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.333 on input line 611. [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.334 on input line 633. Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.335 on input line 660. Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.336 on input line 685. Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.337 on input line 707. ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Package longtable Warning: Column widths have changed (longtable) in table 7.338 on input line 171. Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.339 on input line 232. Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.340 on input line 254. [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.341 on input line 276. Underfull \hbox (badness 10000) detected at line 291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.342 on input line 298. Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Package longtable Warning: Column widths have changed (longtable) in table 7.343 on input line 332. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.344 on input line 357. Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.345 on input line 382. Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.346 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.347 on input line 435. Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Package longtable Warning: Column widths have changed (longtable) in table 7.348 on input line 460. Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.349 on input line 485. Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.350 on input line 510. [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.351 on input line 532. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.352 on input line 557. Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.353 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.354 on input line 607. Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.355 on input line 632. Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.356 on input line 657. [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.357 on input line 682. Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.358 on input line 707. Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.359 on input line 732. Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.360 on input line 757. Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.361 on input line 782. Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.362 on input line 807. Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.363 on input line 832. Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.364 on input line 857. [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.365 on input line 882. Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.366 on input line 907. Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.367 on input line 932. Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Package longtable Warning: Column widths have changed (longtable) in table 7.368 on input line 49. Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.369 on input line 79. Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.370 on input line 116. ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.371 on input line 150. Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.372 on input line 195. Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Package longtable Warning: Column widths have changed (longtable) in table 7.373 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.374 on input line 253. Underfull \hbox (badness 10000) detected at line 268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.375 on input line 275. [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.376 on input line 301. Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.377 on input line 326. Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Package longtable Warning: Column widths have changed (longtable) in table 7.378 on input line 351. Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.379 on input line 376. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.380 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.381 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.382 on input line 452. Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.383 on input line 488. Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.384 on input line 527. Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.385 on input line 560. Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.386 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.387 on input line 611. Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.388 on input line 648. [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.389 on input line 682. Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245] Package longtable Warning: Column widths have changed (longtable) in table 7.390 on input line 721. ) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Package longtable Warning: Column widths have changed (longtable) in table 7.391 on input line 114. Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.392 on input line 159. Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.393 on input line 192. Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.394 on input line 217. [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.395 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.396 on input line 263. Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.397 on input line 286. Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.398 on input line 311. Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.399 on input line 340. Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.400 on input line 88. Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.401 on input line 119. Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.402 on input line 152. Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.403 on input line 177. [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.404 on input line 199. Underfull \hbox (badness 10000) detected at line 214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.405 on input line 225. Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.406 on input line 254. [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.407 on input line 171. [259] Underfull \hbox (badness 10000) detected at line 186 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.408 on input line 219. [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.412 on input line 401. Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.413 on input line 443. Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.414 on input line 473. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Package longtable Warning: Column widths have changed (longtable) in table 7.415 on input line 505. Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.416 on input line 535. Underfull \hbox (badness 10000) detected at line 546 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.417 on input line 561. [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.418 on input line 583. Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Package longtable Warning: Column widths have changed (longtable) in table 7.419 on input line 619. Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.420 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.421 on input line 675. [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.422 on input line 697. Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.423 on input line 727. [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.424 on input line 753. Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.425 on input line 784. [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.426 on input line 841. [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.427 on input line 879. Underfull \hbox (badness 10000) detected at line 894 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.428 on input line 909. [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.429 on input line 941. Underfull \hbox (badness 10000) detected at line 956 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.430 on input line 971. [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.431 on input line 997. Underfull \hbox (badness 10000) detected at line 1008 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.432 on input line 1019. [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.433 on input line 1040. Underfull \hbox (badness 10000) detected at line 1055 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.434 on input line 1076. [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.435 on input line 1108. [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.436 on input line 1140. Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.437 on input line 1175. [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.438 on input line 1211. Underfull \hbox (badness 10000) detected at line 1226 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.439 on input line 1241. [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.440 on input line 1269. Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.441 on input line 1292. Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.442 on input line 1316. Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Package longtable Warning: Column widths have changed (longtable) in table 7.443 on input line 1358. Underfull \hbox (badness 10000) detected at line 1373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.444 on input line 1386. Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.445 on input line 1411. [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.446 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.447 on input line 1461. ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.448 on input line 85. Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.449 on input line 112. Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Package longtable Warning: Column widths have changed (longtable) in table 7.450 on input line 137. Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.451 on input line 159. Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.452 on input line 193. [285] Underfull \hbox (badness 10000) detected at line 208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.453 on input line 215. ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.454 on input line 293. [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.455 on input line 324. Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.457 on input line 631. [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.458 on input line 704. [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.459 on input line 757. [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1567. [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1713. Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.467 on input line 1751. [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.468 on input line 1788. Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Package longtable Warning: Column widths have changed (longtable) in table 7.469 on input line 1825. Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.470 on input line 1862. [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2016. [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.472 on input line 2053. [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.473 on input line 2188. [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.474 on input line 2227. [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2266. Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.476 on input line 2297. [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2486. [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2680. [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2729. Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2888. Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.481 on input line 2929. [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3029. [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.483 on input line 3170. [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3325. [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3416. [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3525. Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.487 on input line 3568. [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3772. [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3873. [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.490 on input line 3955. Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.491 on input line 3984. [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.492 on input line 4017. [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4177. [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4273. Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4366. [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.496 on input line 4409. Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Package longtable Warning: Column widths have changed (longtable) in table 7.497 on input line 4454. Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4515. [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4679. [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.500 on input line 4710. [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.501 on input line 4751. Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4913. [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.503 on input line 4948. Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.504 on input line 5084. [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.505 on input line 5120. Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.506 on input line 5153. [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.507 on input line 5186. Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.508 on input line 5217. Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.509 on input line 5248. [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.510 on input line 5281. ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.511 on input line 196. Underfull \hbox (badness 10000) detected at line 211 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.512 on input line 232. [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.513 on input line 260. Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.514 on input line 296. [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.515 on input line 336. [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.516 on input line 372. Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] Package longtable Warning: Column widths have changed (longtable) in table 7.517 on input line 480. [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.518 on input line 557. [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.519 on input line 610. [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.520 on input line 634. Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.521 on input line 662. Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.522 on input line 705. Underfull \hbox (badness 10000) detected at line 720 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.523 on input line 733. [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.524 on input line 757. Underfull \hbox (badness 10000) detected at line 772 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.525 on input line 781. Underfull \hbox (badness 10000) detected at line 792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.526 on input line 803. [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.527 on input line 827. Underfull \hbox (badness 10000) detected at line 842 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.528 on input line 851. Underfull \hbox (badness 10000) detected at line 866 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.529 on input line 875. [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.530 on input line 908. Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.531 on input line 938. [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.532 on input line 970. Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.533 on input line 995. [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.534 on input line 1020. Underfull \hbox (badness 10000) detected at line 1035 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.535 on input line 1044. Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.536 on input line 1076. Underfull \hbox (badness 10000) detected at line 1091 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.537 on input line 1104. Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.538 on input line 1133. Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.539 on input line 1151. Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.540 on input line 1179. Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.541 on input line 1213. Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.542 on input line 1244. [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.543 on input line 1273. Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.544 on input line 1304. [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.545 on input line 1333. Underfull \hbox (badness 10000) detected at line 1348 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.546 on input line 1362. [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.547 on input line 1393. Underfull \hbox (badness 10000) detected at line 1408 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.548 on input line 1417. Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.549 on input line 1439. [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.550 on input line 1467. Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.551 on input line 1496. Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.552 on input line 1527. Underfull \hbox (badness 10000) detected at line 1528 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.553 on input line 1547. Underfull \hbox (badness 10000) detected at line 1562 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.554 on input line 1573. [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.555 on input line 1621. [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.556 on input line 1649. Underfull \hbox (badness 10000) detected at line 1650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.557 on input line 1673. Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Package longtable Warning: Column widths have changed (longtable) in table 7.558 on input line 1715. Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.559 on input line 1746. Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.560 on input line 1791. Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.561 on input line 1822. [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.1 on input line 124. [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.2 on input line 187. Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.3 on input line 218. Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.4 on input line 182. [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.5 on input line 172. ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.6 on input line 313. [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 388. Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 438. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 463. [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 488. Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 513. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.13 on input line 855. Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Package longtable Warning: Column widths have changed (longtable) in table 9.14 on input line 885. Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Package longtable Warning: Column widths have changed (longtable) in table 9.15 on input line 927. Underfull \hbox (badness 10000) detected at line 942 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.16 on input line 949. Underfull \hbox (badness 10000) detected at line 964 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.17 on input line 971. [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.18 on input line 1016. Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.19 on input line 1041. [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.20 on input line 1066. Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.21 on input line 1125. Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.22 on input line 1152. ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.23 on input line 442. [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 492. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 517. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 542. [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 567. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.30 on input line 930. [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.31 on input line 960. Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Package longtable Warning: Column widths have changed (longtable) in table 9.32 on input line 982. Underfull \hbox (badness 10000) detected at line 997 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.33 on input line 1004. Underfull \hbox (badness 10000) detected at line 1019 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.34 on input line 1026. [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.35 on input line 1071. Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.36 on input line 1096. [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.37 on input line 1121. Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.38 on input line 1180. Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.39 on input line 1207. ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) 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[1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox 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Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1406 pages, 5228398 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2021] (kpathsea + Thai support). Scanning input file refman.idx.......done (3686 entries accepted, 0 rejected). Sorting entries....................................done (49276 comparisons). 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\hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] [24] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [25] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Overfull \vbox (8.04509pt too high) has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1567. [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1713. Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2016. [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2266. Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2486. [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2680. [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2729. Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2888. Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3029. [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3325. [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3416. [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3525. Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3772. [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3873. [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4177. [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4273. Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4366. [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4515. [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4679. [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4913. [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 388. Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 438. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 463. [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 488. Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 513. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 492. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 517. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 542. [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 567. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 84--85 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1325] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./routines_8c_source.tex [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int 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Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1511 pages, 5646963 bytes). Transcript written on refman.log. Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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\hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] [24] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [25] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Overfull \vbox (8.04509pt too high) has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Underfull \hbox (badness 10000) detected at line 324 [][][] [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] 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[1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1396] Underfull \hbox (badness 2495) in paragraph at lines 112--113 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1397] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] [1398]) (./routines_8h_source.tex [1399] [1400] [1401] [1402]) [1403] [1404] (./refman.ind [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] 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This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-05-07> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array-2016-10-06.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) All fixes are now in the LaTeX kernel. 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has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Underfull \hbox (badness 10000) detected at line 324 [][][] [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 84--85 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1325] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./routines_8c_source.tex [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1396] Underfull \hbox (badness 2495) in paragraph at lines 112--113 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1397] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] [1398]) (./routines_8h_source.tex [1399] [1400] [1401] [1402]) [1403] [1404] (./refman.ind [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1511 pages, 5646846 bytes). Transcript written on refman.log. make[3]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/latex' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 55%] Built target doc-pdf make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 56%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 57%] Linking C executable ../bin/mgmesh make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 57%] Built target mgmesh make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 58%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:163:8: warning: 'format' may be used uninitialized [-Wmaybe-uninitialized] 163 | if (format == VDF_DX) { | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:66:18: note: 'format' was declared here 66 | Vdata_Format format; int gotFormat = 0; | ^~~~~~ [ 59%] Linking C executable ../bin/smooth make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 59%] Built target smooth make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 60%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:41:10: warning: unused variable 'format' [-Wunused-variable] 41 | char format[VMAX_BUFSIZE]; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 62%] Linking C executable ../bin/dxmath make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 62%] Built target dxmath make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 63%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: 'nx' may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:9: note: 'nx' was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: 'nz' may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:17: note: 'nz' was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: 'ny' may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:13: note: 'ny' was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ [ 64%] Linking C executable ../bin/mergedx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 64%] Built target mergedx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 65%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 66%] Linking C executable ../bin/mergedx2 make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 66%] Built target mergedx2 make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 67%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:37:9: warning: unused variable 'inorm' [-Wunused-variable] 37 | int inorm; | ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 68%] Linking C executable ../bin/value make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 68%] Built target value make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 70%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 71%] Linking C executable ../bin/multivalue make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 71%] Built target multivalue make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 72%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:28:12: warning: unused variable 'grid' [-Wunused-variable] 28 | Vgrid *grid; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:58: warning: unused variable 'sum' [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:51: warning: unused variable 'value' [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:44: warning: unused variable 'pt' [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:38: warning: variable 'zmin' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:32: warning: variable 'ymin' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:26: warning: variable 'xmin' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:20: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:16: warning: variable 'hx' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:12: warning: variable 'hy' set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:27: warning: unused variable 'k' [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:24: warning: unused variable 'j' [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:21: warning: unused variable 'i' [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 73%] Linking C executable ../bin/benchmark make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 73%] Built target benchmark make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 74%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:298:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 298 | strncpy(scalar1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:305:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 305 | strncpy(scalar2Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:312:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 312 | strncpy(transformPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:322:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 322 | strncpy(mask1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:329:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 329 | strncpy(mask2Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:452:14: warning: 'format' may be used uninitialized [-Wmaybe-uninitialized] 452 | if (!readGrid(&mask2, mask2Path, format)) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:270:18: note: 'format' was declared here 270 | Vdata_Format format; | ^~~~~~ [ 75%] Linking C executable ../bin/similarity make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 75%] Built target similarity make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 77%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:123:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 123 | strncpy(scalarPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:133:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 133 | strncpy(maskPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[2]' may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: 'minG2pt[2]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[1]' may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: 'minG2pt[1]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[0]' may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: 'minG2pt[0]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[2]' may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: 'minSpt[2]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[1]' may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: 'minSpt[1]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[0]' may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: 'minSpt[0]' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[2]' may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: 'maxG2pt[2]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[0]' may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: 'maxSpt[0]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[1]' may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: 'maxG2pt[1]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[0]' may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: 'maxG2pt[0]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[2]' may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: 'maxSpt[2]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[1]' may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: 'maxSpt[1]' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:290:5: warning: 'minG2' may be used uninitialized [-Wmaybe-uninitialized] 290 | Vnm_print(1, "Min gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | minG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:29: note: 'minG2' was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:286:5: warning: 'maxG2' may be used uninitialized [-Wmaybe-uninitialized] 286 | Vnm_print(1, "Max gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | maxG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:29: note: 'maxG2' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:278:5: warning: 'maxS' may be used uninitialized [-Wmaybe-uninitialized] 278 | Vnm_print(1, "Max scalar value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 | maxS); | ~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:12: note: 'maxS' was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~ [ 78%] Linking C executable ../bin/analysis make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 78%] Built target analysis make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 79%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:28:12: warning: unused variable 'avg' [-Wunused-variable] 28 | double avg; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 80%] Linking C executable ../bin/dx2mol make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 80%] Built target dx2mol make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 81%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:25:10: warning: unused variable 'avg' [-Wunused-variable] 25 | double avg; | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:19: warning: unused variable 'k' [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:16: warning: unused variable 'j' [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:13: warning: unused variable 'i' [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:10: warning: unused variable 'u' [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 82%] Linking C executable ../bin/dx2uhbd make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 82%] Built target dx2uhbd make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 83%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:64: warning: variable 'extent' set but not used [-Wunused-but-set-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:50: warning: unused variable 'xdata' [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:15: warning: unused variable 'val' [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:76:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:89:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:97:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:103:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:106:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Linking C executable ../bin/del2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 85%] Built target del2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 86%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:19: warning: unused variable 'index' [-Wunused-variable] 42 | int i,j,k,index,icol; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:17: warning: unused variable 'k' [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:15: warning: unused variable 'j' [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking C executable ../bin/tensor2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 87%] Built target tensor2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 88%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_grid' [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:24:5: note: in expansion of macro 'MAT3' 24 | MAT3(grid, MXGRD, MXGRD, MXGRD); | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Linking C executable ../bin/uhbd_asc2bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 89%] Built target uhbd_asc2bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 90%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:20:12: warning: unused variable 'j' [-Wunused-variable] 20 | int i, j; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:18:34: warning: unused variable 'disp' [-Wunused-variable] 18 | double *pos, energy, zmagic, disp[3], force[3]; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 91%] Linking C executable ../bin/coulomb make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 91%] Built target coulomb make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 93%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 94%] Linking C executable ../bin/born make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 94%] Built target born make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Scanning dependencies of target apbslib_swig_compilation make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Swig compile apbslib.i for python make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Built target apbslib_swig_compilation make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 96%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function 'getPotentials': /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3264:12: warning: unused variable 'rc' [-Wunused-variable] 3264 | int i, rc, nx, ny, nz; | ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function 'getForces': /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3318:31: warning: unused variable 'npholder' [-Wunused-variable] 3318 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3318:26: warning: unused variable 'np' [-Wunused-variable] 3318 | PyObject *npvalues, *np, *npholder; | ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3318:15: warning: unused variable 'npvalues' [-Wunused-variable] 3318 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:2727: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 97%] Linking C shared library ../../lib/_apbslib.so /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:267:26: note: in a call to function 'Vparam_getAtomData' 267 | VPUBLIC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:267:26: note: in a call to function 'Vparam_getAtomData' 267 | VPUBLIC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:267:26: note: in a call to function 'Vparam_getAtomData' 267 | VPUBLIC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type 'char[1024]' /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:267:26: note: in a call to function 'Vparam_getAtomData' 267 | VPUBLIC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 97%] Built target _apbslib make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 98%] Building C object contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:57:21: warning: argument 23 of type 'double[1]' with mismatched bound [-Warray-parameter=] 57 | double esenergy[1], | ~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:19: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:173:30: note: previously declared as 'double[20]' 173 | double esEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:58:21: warning: argument 24 of type 'double[1]' with mismatched bound [-Warray-parameter=] 58 | double npenergy[1], | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:174:30: note: previously declared as 'double[20]' 174 | double npEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'apbsdrv_': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:278:5: warning: multi-line comment [-Wcomment] 278 | // Vnm_print(1,"\nError you must provide a parameter file if you\n" \ | ^ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:110:21: warning: unused variable 'isolve' [-Wunused-variable] 110 | int rank, size, isolve, debug, natom; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:98:11: warning: unused variable 'gm' [-Wunused-variable] 98 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:97:11: warning: variable 'fetk' set but not used [-Wunused-but-set-variable] 97 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:85:14: warning: unused variable 'feparm' [-Wunused-variable] 85 | FEMparm *feparm = VNULL; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'setupString': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:64: warning: implicit declaration of function 'getpid' [-Wimplicit-function-declaration] 938 | sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'setupString': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:26: warning: 'write pot dx iapbs-pot-' directive writing 23 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 938 | sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function 'sprintf', inlined from 'setupString' at /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:7: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 26 and 4131 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/bits/stdio2.h:30:10: warning: '__sprintf_chk' argument 5 overlaps destination object 'string.1' [-Wrestrict] /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'setupString': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:798:17: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 798 | static char string[MAX_BUF_SIZE]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'getElecEnergy': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1055:29: warning: 'scalar' may be used uninitialized [-Wmaybe-uninitialized] 1055 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1038:32: note: 'scalar' was declared here 1038 | double ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'apbsdrv_': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:549:56: warning: 'outputformat' may be used uninitialized [-Wmaybe-uninitialized] 549 | if ((pbeparm->calcenergy == PCE_COMPS) && (outputformat != OUTPUT_NULL)){ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:113:20: note: 'outputformat' was declared here 113 | Voutput_Format outputformat; | ^~~~~~~~~~~~ [100%] Linking C static library ../../../lib/libiapbs.a make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [100%] Built target iapbs make[1]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.lL3nLs + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 ++ dirname /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/apbs-3.0.0/.package_note-apbs-3.0.0-16.fc37.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 'INSTALL=/usr/bin/install -p' -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[1]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_mg make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 5%] Built target apbs_mg make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_generic make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 26%] Built target apbs_generic make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_pmgc make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 47%] Built target apbs_pmgc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 48%] Built target apbs make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_routines make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 49%] Built target apbs_routines make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs-bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 52%] Built target apbs-bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Generating documentation with Doxygen warning: Tag 'TCL_SUBST' at line 213 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 857 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1313 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1565 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1577 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1586 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' does not exist warning: source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' is not a readable file or directory... skipping. Doxygen version used: 1.9.4 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/fem Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/generic Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/mg Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/pmgc Reading formula repository... Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... 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Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vstring.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vstring.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vstring.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vstring.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/generic/vunit.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/generic/vunit.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/main.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/main.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Parsing file /builddir/build/builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.h:7: warning: the name 'beparm.h' supplied as the argument in the \file statement is not an input file /BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating images for formulas in HTML... Generating example documentation... Generating file sources... Generating code for file doc/programmer/mainpage.h... Generating code for file src/apbs.h... Generating code for file src/fem/vcsm.c... Generating code for file src/fem/vcsm.h... Generating code for file src/fem/vfetk.c... Generating code for file src/fem/vfetk.h... Generating code for file src/fem/vpee.c... Generating code for file src/fem/vpee.h... Generating code for file src/generic/apolparm.c... Generating code for file src/generic/apolparm.h... Generating code for file src/generic/bemparm.c... Generating code for file src/generic/bemparm.h... Generating code for file src/generic/femparm.c... Generatin/builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:2095: warning: Member polyEval(int numP, double p[], double c[][VMAXP], double xv[]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1528: warning: Member Vfetk_PDE_initElement(PDE *thee, int elementType, int chart, double tvx[][3], void *data) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1571: warning: Member Vfetk_PDE_initPoint(PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1741: warning: Member Vfetk_PDE_DFu_wv(PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1902: warning: Member Vfetk_PDE_bisectEdge(int dim, int dimII, int edgeType, int chart[], double vx[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1912: warning: Member Vfetk_PDE_mapBoundary(int dim, int dimII, int vertexType, int chart, double vx[3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1917: warning: Member Vfetk_PDE_markSimplex(int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1998: warning: Member Vfetk_PDE_oneChart(int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:86: warning: Member var (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:93: warning: Member diriCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:130: warning: Member neumCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:366: warning: Member dim_2DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:386: warning: Member lgr_2DP1[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:395: warning: Member lgr_2DP1x[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:402: warning: Member lgr_2DP1y[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:409: warning: Member lgr_2DP1z[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:437: warning: Member dim_3DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:438: warning: Member lgr_3DP1[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:446: warning: Member lgr_3DP1x[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:454: warning: Member lgr_3DP1y[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:462: warning: Member lgr_3DP1z[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:476: warning: Member P_DEG (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:482: warning: Member numP (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:483: warning: Member c[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:484: warning: Member cx[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:485: warning: Member cy[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:486: warning: Member cz[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. g code for file src/generic/femparm.h... Generating code for file src/generic/geoflowparm.c... Generating code for file src/generic/geoflowparm.h... Generating code for file src/generic/mgparm.c... Generating code for file src/generic/mgparm.h... Generating code for file src/generic/nosh.c... Generating code for file src/generic/nosh.h... Generating code for file src/generic/pbamparm.c... Generating code for file src/generic/pbamparm.h... Generating code for file src/generic/pbeparm.c... Generating code for file src/generic/pbeparm.h... Generating code for file src/generic/pbsamparm.c... Generating code for file src/generic/pbsamparm.h... Generating code for file src/generic/vacc.c... Generating code for file src/generic/vacc.h... Generating code for file src/generic/valist.c... Generating code for file src/generic/valist.h... Generating code for file src/generic/vatom.c... Generating code for file src/generic/vatom.h... Generating code for file src/generic/vcap.c... Generating code for file src/generic/vcap.h... Generating code for file src/generic/vclist.c... Generating code for file src/generic/vclist.h... Generating code for file src/generic/vgreen.c... Generating code for file src/generic/vgreen.h... Generating code for file src/generic/vhal.h... Generating code for file src/generic/vmatrix.h... Generating code for file src/generic/vparam.c... Generating code for file src/generic/vparam.h... Generating code for file src/generic/vpbe.c... Generating code for file src/generic/vpbe.h... Generating code for file src/generic/vstring.c... Generating code for file src/generic/vstring.h... Generating code for file src/generic/vunit.h... Generating code for file src/main.c... Generating code for file src/mg/vgrid.c... Generating code for file src/mg/vgrid.h... Generating code for file src/mg/vmgrid.c... Generating code for file src/mg/vmgrid.h... Generating code for file src/mg/vopot.c... Generating code for file src/mg/vopot.h... Generating code for file src/mg/vpmg.c... Generating code for file src/mg/vpmg.h... Generating code for file src/mg/vpmgp.c... Generating code for file src/mg/vpmgp.h... Generating code for file src/pmgc/buildAd.c... Generating code for file src/pmgc/buildAd.h... Generating code for file src/pmgc/buildBd.c... Generating code for file src/pmgc/buildBd.h... Generating code for file src/pmgc/buildGd.c... Generating code for file src/pmgc/buildGd.h... Generating code for file src/pmgc/buildPd.c... Generating code for file src/pmgc/buildPd.h... Generating code for file src/pmgc/cgd.c... Generating code for file src/pmgc/cgd.h... Generating code for file src/pmgc/gsd.c... Generating code for file src/pmgc/gsd.h... Generating code for file src/pmgc/matvecd.c... Generating code for file src/pmgc/matvecd.h... Generating code for file src/pmgc/mgcsd.c... Generating code for file src/pmgc/mgcsd.h... Generating code for file src/pmgc/mgdrvd.c... Generating code for file src/pmgc/mgdrvd.h... Generating code for file src/pmgc/mgfasd.c... Generating code for file src/pmgc/mgfasd.h... Generating code for file src/pmgc/mgsubd.c... Generating code for file src/pmgc/mgsubd.h... Generating code for file src/pmgc/mikpckd.c... Generating code for file src/pmgc/mikpckd.h... Generating code for file src/pmgc/mlinpckd.c... Generating code for file src/pmgc/mlinpckd.h... Generating code for file src/pmgc/mypdec.c... Generating code for file src/pmgc/mypdec.h... Generating code for file src/pmgc/newdrvd.c... Generating code for file src/pmgc/newdrvd.h... Generating code for file src/pmgc/newtond.c... Generating code for file src/pmgc/newtond.h... Generating code for file src/pmgc/powerd.c... Generating code for file src/pmgc/powerd.h... Generating code for file src/pmgc/smoothd.c... Generating code for file src/pmgc/smoothd.h... Generating code for file src/routines.c... Generating code for file src/routines.h... Generating file documentation... Generating docs for file src/apbs.h... Generating docs for file src/fem/vcsm.c... Generating docs for file src/fem/vcsm.h... Generating docs for file src/fem/vfetk.c... Generating do/builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:498: warning: Member Vpee_userDefined(Vpee *thee, SS *sm) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:532: warning: Member Vpee_ourSimp(Vpee *thee, SS *sm, int rcol) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:66: warning: Member Aprx_estNonlinResid(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:72: warning: Member Aprx_estLocalProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:77: warning: Member Aprx_estDualProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:237: warning: Member APOLparm_parseGRID(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:268: warning: Member APOLparm_parseMOL(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:287: warning: Member APOLparm_parseSRFM(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:309: warning: Member APOLparm_parseSRAD(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:328: warning: Member APOLparm_parseSWIN(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:347: warning: Member APOLparm_parseTEMP(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:366: warning: Member APOLparm_parseGAMMA(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:385: warning: Member APOLparm_parseCALCENERGY(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:438: warning: Member APOLparm_parseCALCFORCE(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:491: warning: Member APOLparm_parseBCONC(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:510: warning: Member APOLparm_parseSDENS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:529: warning: Member APOLparm_parseDPOS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:558: warning: Member APOLparm_parsePRESS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:210: warning: Member BEMparm_parseTREE_ORDER(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:233: warning: Member BEMparm_parseTREE_N0(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:256: warning: Member BEMparm_parseMAC(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:279: warning: Member BEMparm_parseMESH(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:308: warning: Member BEMparm_parseOUTDATA(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:196: warning: Member FEMparm_parseDOMAINLENGTH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:221: warning: Member FEMparm_parseETOL(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:244: warning: Member FEMparm_parseEKEY(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:276: warning: Member FEMparm_parseAKEYPRE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:303: warning: Member FEMparm_parseAKEYSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:333: warning: Member FEMparm_parseTARGETNUM(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:352: warning: Member FEMparm_parseTARGETRES(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:372: warning: Member FEMparm_parseMAXSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:391: warning: Member FEMparm_parseMAXVERT(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:411: warning: Member FEMparm_parseUSEMESH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:138: warning: Member FUBAR(const char *name) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:143: warning: Member parseNonNeg(double *tf, double def, int *set, char *name, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:164: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:186: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:415: warning: Member MGparm_parseDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:446: warning: Member MGparm_parseCHGM(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:497: warning: Member MGparm_parseNLEV(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:516: warning: Member MGparm_parseETOL(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:539: warning: Member MGparm_parseGRID(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:570: warning: Member MGparm_parseGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:601: warning: Member MGparm_parseGAMMA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:616: warning: Member MGparm_parseGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:668: warning: Member MGparm_parseCGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:699: warning: Member MGparm_parseFGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:730: warning: Member MGparm_parseCGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:782: warning: Member MGparm_parseFGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:834: warning: Member MGparm_parsePDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:872: warning: Member MGparm_parseOFRAC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:892: warning: Member MGparm_parseASYNC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:912: warning: Member MGparm_parseUSEAQUA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:970: warning: Member NOsh_parseREAD(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1021: warning: Member NOsh_parsePRINT(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1187: warning: Member NOsh_parseELEC(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1313: warning: Member NOsh_parseAPOLAR(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2385: warning: Member NOsh_parseFEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1510: warning: Member NOsh_parseMG(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2845: warning: Member NOsh_parseBEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2934: warning: Member NOsh_parseGEOFLOW(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3048: warning: Member NOsh_parsePBAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3166: warning: Member NOsh_parsePBSAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2508: warning: Member NOsh_parseAPOL(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1603: warning: Member NOsh_setupCalcMG(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1815: warning: Member NOsh_setupCalcMGAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1747: warning: Member NOsh_setupCalcMGMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2090: warning: Member NOsh_setupCalcMGPARA(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1722: warning: Member NOsh_setupCalcFEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2471: warning: Member NOsh_setupCalcFEMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1638: warning: Member NOsh_setupCalcBEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1666: warning: Member NOsh_setupCalcGEOFLOW(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1686: warning: Member NOsh_setupCalcPBAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1704: warning: Member NOsh_setupCalcPBSAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2612: warning: Member NOsh_setupCalcBEMMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2677: warning: Member NOsh_setupCalcGEOFLOWMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2735: warning: Member NOsh_setupCalcPBAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2786: warning: Member NOsh_setupCalcPBSAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2581: warning: Member NOsh_setupCalcAPOL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:598: warning: Member NOsh_parseREAD_MOL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:675: warning: Member NOsh_parseREAD_PARM(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:739: warning: Member NOsh_parseREAD_DIEL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:793: warning: Member NOsh_parseREAD_KAPPA(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:839: warning: Member NOsh_parseREAD_POTENTIAL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:884: warning: Member NOsh_parseREAD_CHARGE(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:930: warning: Member NOsh_parseREAD_MESH(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:458: warning: Member PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:549: warning: Member PBAMparm_parseTerm(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:77: warning: Member PBAMPARM_MAXWRITE (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:78: warning: Member PBAMPARM_MAXMOL (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:87: warning: Member PBEparm_getzmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:91: warning: Member PBEparm_getLmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:95: warning: Member PBEparm_getmembraneDiel(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:99: warning: Member PBEparm_getmemv(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:368: warning: Member PBEparm_parseLPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:375: warning: Member PBEparm_parseNPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:382: warning: Member PBEparm_parseMOL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:401: warning: Member PBEparm_parseLRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:408: warning: Member PBEparm_parseNRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:415: warning: Member PBEparm_parseSMPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:474: warning: Member PBEparm_parseBCFL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:555: warning: Member PBEparm_parseION(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:652: warning: Member PBEparm_parsePDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:671: warning: Member PBEparm_parseSDENS(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:690: warning: Member PBEparm_parseSDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:709: warning: Member PBEparm_parseSRFM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:780: warning: Member PBEparm_parseSRAD(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:799: warning: Member PBEparm_parseSWIN(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:818: warning: Member PBEparm_parseTEMP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:837: warning: Member PBEparm_parseUSEMAP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:895: warning: Member PBEparm_parseCALCENERGY(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:948: warning: Member PBEparm_parseCALCFORCE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1005: warning: Member PBEparm_parseZMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1025: warning: Member PBEparm_parseLMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1044: warning: Member PBEparm_parseMDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1063: warning: Member PBEparm_parseMEMV(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1084: warning: Member PBEparm_parseWRITE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1178: warning: Member PBEparm_parseWRITEMAT(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:77: warning: Member PBSAMPARM_MAXWRITE (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:78: warning: Member PBSAMPARM_MAXMOL (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:277: warning: Member Vacc_vdwAcc(Vacc *thee, double center[3]) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:307: warning: Member Vacc_ivdwAcc(Vacc *thee, double center[3], double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:679: warning: Member Vacc_writeGMV(Vacc *thee, double radius, int meth, Gem *gm, char *iodev, char *iofmt, char *iohost, char *iofile) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1252: warning: Member Vacc_SASAPos(Vacc *thee, double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1277: warning: Member Vacc_atomSASAPos(Vacc *thee, double radius, Vatom *atom, int mode) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:76: warning: The following parameter of ivdwAccExclus(Vacc *thee, double center[3], double radius, int atomID) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:490: warning: The following parameter of splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:186: warning: Member Valist_readPDBSerial(Valist *thee, Vio *sock, int *serial) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:206: warning: Member Valist_readPDBAtomName(Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:224: warning: Member Valist_readPDBResidueName(Valist *thee, Vio *sock, char resName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:242: warning: Member Valist_readPDBResidueNumber(Valist *thee, Vio *sock, int *resSeq) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:298: warning: Member Valist_readPDBAtomCoord(Valist *thee, Vio *sock, double *coord) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:316: warning: Member Valist_readPDBChargeRadius(Valist *thee, Vio *sock, double *charge, double *radius) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:344: warning: Member Valist_readPDB_throughXYZ(Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:424: warning: Member Valist_getAtomStorage(Valist *thee, Vatom **plist, int *pnlist, int *pnatoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:480: warning: Member Valist_setAtomArray(Valist *thee, Vatom **plist, int nlist, int natoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:60: warning: Member Valist_whiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:61: warning: Member Valist_commChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:62: warning: Member Valist_xmlwhiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:128: warning: Member VCLIST_INFLATE (macro definition) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:90: warning: Member Vclist_getMolDims(Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:125: warning: Member Vclist_setupGrid(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:174: warning: Member Vclist_storeParms(Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:231: warning: Member Vclist_gridSpan(Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:262: warning: Member Vclist_arrayIndex(Vclist *thee, int i, int j, int k) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:270: warning: Member Vclist_assignAtoms(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425: warning: Member treesetup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505: warning: Member treecleanup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525: warning: Member treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, double *qtar, int numtars, double *tpengtar, double *x, double *y, double *z, double *q, int numpars, double *fx, double *fy, double *fz, int iflag, int farrdim, int arrdim) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:458: warning: Member MAX_HASH_DIM (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:572: warning: Member OS_SEP_STR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:573: warning: Member OS_SEP_CHAR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:600: warning: Member ANNOUNCE_FUNCTION (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:601: warning: Member WARN_UNTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:602: warning: Member WARN_PARTTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:653: warning: Member VCHANNELEDMESSAGE0(channel, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:658: warning: Member VCHANNELEDMESSAGE1(channel, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:665: warning: Member VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:672: warning: Member VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:679: warning: Member VMESSAGE0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:680: warning: Member VMESSAGE1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:681: warning: Member VMESSAGE2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:682: warning: Member VMESSAGE3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:684: warning: Member VERRMSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:685: warning: Member VERRMSG1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:686: warning: Member VERRMSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:687: warning: Member VERRMSG3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:731: warning: Member VASSERT_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:741: warning: Member VASSERT_MSG1(cnd, msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:753: warning: Member VASSERT_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:825: warning: Member VWARN_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:838: warning: Member VWARN_MSG1(cnd, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:853: warning: Member VWARN_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:899: warning: Member VABORT_MSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:907: warning: Member VABORT_MSG1(msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:917: warning: Member VABORT_MSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:944: warning: Member PRINT_INT(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:945: warning: Member PRINT_DBL(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:948: warning: Member VMALLOC(vmem, n, type) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:950: warning: Member VFREE(vmem, n, type, ptr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:952: warning: Member VFILL(vec, n, val) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:959: warning: Member VCOPY(srcvec, dstvec, i, n) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:968: warning: Member VAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:969: warning: Member RAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:73: warning: Member Vrc_Codes (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:95: warning: Member Vsol_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:966: warning: Member wrap_text(char *str, int right_margin, int left_padding) (function) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:64: warning: Member MAT2(mat, dx, dy) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:68: warning: Member RAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:71: warning: Member VAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:76: warning: Member MAT3(mat, dx, dy, dz) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:81: warning: Member RAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:84: warning: Member VAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c:62: warning: Member MAX_SPLINE_WINDOW (macro definition) of file vpbe.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:67: warning: Member IJK(i, j, k) (macro definition) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:77: warning: Member MCwhiteChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:78: warning: Member MCcommChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:79: warning: Member Vcompare (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:80: warning: Member Vprecision[26] (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:113: warning: Member IJK(i, j, k) (macro definition) of file vopot.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1401: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828: warning: Member bcCalcOrig(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3130: warning: Member gridPointIsValid(int i, int j, int k, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3313: warning: Member packAtoms(double *ax, double *ay, double *az, double *charge, double *size, Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3338: warning: Member packUnpack(int nx, int ny, int nz, int ngrid, double *gx, double *gy, double *gz, double *value, Vpmg *thee, int pack) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3407: warning: Member bcflnew(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3597: warning: Member bcfl_sdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868: warning: Member bcfl_mdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3995: warning: Member bcfl_mem(double zmem, double L, double eps_m, double eps_w, double V, double xkappa, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4174: warning: Member bcfl_map(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684: warning: Member markFrac(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *xarray, double *yarray, double *zarray) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10260: warning: Member fillcoPermanentInduced(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: argument 'hz' of command @param is not found in the argument list of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1107: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:105: warning: Member VPMGMAXPART (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1392: warning: Member VCUB(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1393: warning: Member VLOG(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1395: warning: Member IJK(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1396: warning: Member IJKx(j, k, i) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1397: warning: Member IJKy(i, k, j) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1398: warning: Member IJKz(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1399: warning: Member VFCHI(iint, iflt) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1107: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:294: warning: Member coarsenThis(int nOld) (function) of file vpmgp.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: argument 'parm' of command @param is not found in the argument list of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: The following parameter of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) is not documented: parameter 'sock' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:513: warning: The following parameter of energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) is not documented: parameter 'apolparm' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:610: warning: The following parameter of killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:262: warning: The following parameter of killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: argument 'charge' of command @param is not found in the argument list of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: The following parameter of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: argument 'kappa' of command @param is not found in the argument list of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: The following parameter of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: argument 'pot' of command @param is not found in the argument list of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: The following parameter of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:622: warning: argument 'nosh' of command @param is not found in the argument list of preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/routines.h:494: warning: The following parameter of printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:445: warning: The following parameter of printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:481: warning: The following parameter of printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:432: warning: The following parameter of printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:468: warning: The following parameter of printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4125: warning: argument 'i' of command @param is not found in the argument list of solveFE(int icalc, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:104: warning: Member vdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:105: warning: Member setvdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:111: warning: Member salt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:112: warning: Member setsalt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:115: warning: Member runtype[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:116: warning: Member setruntype (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:119: warning: Member runname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:120: warning: Member setrunname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:123: warning: Member setrandorient (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:126: warning: Member pbcboxlen (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:127: warning: Member setpbcs (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:130: warning: Member units[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:131: warning: Member setunits (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:137: warning: Member gridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:138: warning: Member setgridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:141: warning: Member map3dname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:142: warning: Member set3dmap (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:145: warning: Member grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:146: warning: Member grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:147: warning: Member grid2Dloc[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:148: warning: Member grid2Dct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:149: warning: Member setgrid2Dname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:152: warning: Member dxname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:153: warning: Member setdxname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:158: warning: Member ntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:159: warning: Member setntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:161: warning: Member termcombine[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:162: warning: Member settermcombine (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:164: warning: Member diffct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:165: warning: Member moveType[PBAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:166: warning: Member transDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:167: warning: Member rotDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:169: warning: Member termct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:170: warning: Member setterm (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:172: warning: Member termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:173: warning: Member termnu[PBAMPARM_MAXWRITE][1] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:174: warning: Member termVal[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:175: warning: Member confil[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:176: warning: Member conpad[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:177: warning: Member confilct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:179: warning: Member setxyz (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:180: warning: Member xyzct[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:181: warning: Member xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:202: warning: Member pbam_3dmapstem[VMAX_ARGLEN] (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:203: warning: Member pbam_3dmapflag (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:112: warning: Member settolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:113: warning: Member tolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:115: warning: Member setmsms (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:116: warning: Member probe_radius (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:117: warning: Member density (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:119: warning: Member setsurf (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:120: warning: Member surfct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:121: warning: Member surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:123: warning: Member setimat (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:124: warning: Member imatct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:125: warning: Member imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:127: warning: Member setexp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:128: warning: Member expct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:129: warning: Member expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. cs for file src/fem/vfetk.h... Generating docs for file src/fem/vpee.c... Generating docs for file src/fem/vpee.h... Generating docs for file src/generic/apolparm.c... Generating docs for file src/generic/bemparm.c... Generating docs for file src/generic/femparm.c... Generating docs for file src/generic/femparm.h... Generating docs for file src/generic/geoflowparm.c... Generating docs for file src/generic/geoflowparm.h... Generating docs for file src/generic/mgparm.c... Generating docs for file src/generic/mgparm.h... Generating docs for file src/generic/nosh.c... Generating docs for file src/generic/nosh.h... Generating docs for file src/generic/pbamparm.c... Generating docs for file src/generic/pbamparm.h... Generating docs for file src/generic/pbeparm.c... Generating docs for file src/generic/pbeparm.h... Generating docs for file src/generic/pbsamparm.c... Generating docs for file src/generic/pbsamparm.h... Generating docs for file src/generic/vacc.c... Generating docs for file src/generic/vacc.h... Generating docs for file src/generic/valist.c... Generating docs for file src/generic/valist.h... Generating docs for file src/generic/vatom.c... Generating docs for file src/generic/vatom.h... Generating docs for file src/generic/vcap.c... Generating docs for file src/generic/vcap.h... Generating docs for file src/generic/vclist.c... Generating docs for file src/generic/vclist.h... Generating docs for file src/generic/vgreen.c... Generating docs for file src/generic/vgreen.h... Generating docs for file src/generic/vhal.h... Generating docs for file src/generic/vmatrix.h... Generating docs for file src/generic/vparam.c... Generating docs for file src/generic/vparam.h... Generating docs for file src/generic/vpbe.c... Generating docs for file src/generic/vpbe.h... Generating docs for file src/generic/vstring.c... Generating docs for file src/generic/vstring.h... Generating docs for file src/generic/vunit.h... Generating docs for file src/main.c... Generating docs for file src/mg/vgrid.c... Generating docs for file src/mg/vgrid.h... Generating docs for file src/mg/vmgrid.c... Generating docs for file src/mg/vmgrid.h... Generating docs for file src/mg/vopot.c... Generating docs for file src/mg/vopot.h... Generating docs for file src/mg/vpmg.c... Generating docs for file src/mg/vpmg.h... Generating docs for file src/mg/vpmgp.c... Generating docs for file src/mg/vpmgp.h... Generating docs for file src/routines.c... Generating docs for file src/routines.h... Generating page documentation... Generating docs for page bug... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound AtomForce... Generating docs for compound sAPOLparm... Generating docs for compound sBEMparm... Generating docs for compound sFEMparm... Generating docs for compound sGEOFLOWparm... Generating docs for compound sMGparm... Generating docs for compound sNOsh... Generating docs for compound sNOsh_calc... Generating docs for compound sPBAMparm... Generating docs for compound sPBEparm... Generating docs for compound sPBSAMparm... Generating docs for compound sVacc... Generating docs for compound sVaccSurf... Generating docs for compound sValist... Generating docs for compound sVatom... Generating docs for compound sVclist... Generating docs for compound sVclistCell... Generating docs for compound sVcsm... Generating docs for compound sVfetk... Generating docs for compound sVfetk_LocalVar... Generating docs for compound sVgreen... Generating docs for compound sVgrid... Generating docs for compound sVmgrid... Generating docs for compound sVopot... Generating docs for compound sVparam_AtomData... Generating docs for compound sVpbe... Generating docs for compound sVpee... Generating docs for compound sVpmg... Generating docs for compound sVpmgp... Generating docs for compound Vparam... Generating docs for compound Vparam_ResData... Generating concept documentation... Generating namespace index... Generating graph info page... Generating directory documentation... Generating dependency grerror: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apolparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/bemparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/femparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/geoflowparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/mgparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/nosh_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbamparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbeparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/pbsamparm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/main_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/valist_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vacc_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vatom_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcap_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/routines_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vclist_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vcsm_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vfetk_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgreen_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vgrid_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmgrid_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vmatrix_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vhal_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vopot_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vparam_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpbe_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpee_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmgp_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vstring_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vunit_8h__dep__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8c__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.pdf /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.dot:1: error: Problems running dot: exit code=0, command='dot', arguments='"/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.dot" -Tpdf -o "/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/vpmg_8h__incl.pdf"' error: Failed to extract bounding box from generated diagram file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/./latex/apbs_8h__incl.pdf error: problem writing FIG 0 figure! aph for directory src/fem Generating dependency graph for directory src/generic Generating dependency graph for directory src/mg Generating dependency graph for directory src/pmgc Generating dependency graph for directory doc/programmer Generating dependency graph for directory src Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 6 parallel threads... Running dot for graph 1/84 Running dot for graph 2/84 Running dot for graph 3/84 Running dot for graph 4/84 Running dot for graph 5/84 Running dot for graph 6/84 Running dot for graph 7/84 Running dot for graph 8/84 Running dot for graph 9/84 Running dot for graph 10/84 Running dot for graph 11/84 Running dot for graph 12/84 Running dot for graph 13/84 Running dot for graph 14/84 Running dot for graph 15/84 Running dot for graph 16/84 Running dot for graph 17/84 Running dot for graph 18/84 Running dot for graph 19/84 Running dot for graph 20/84 Running dot for graph 21/84 Running dot for graph 22/84 Running dot for graph 23/84 Running dot for graph 24/84 Running dot for graph 25/84 Running dot for graph 26/84 Running dot for graph 27/84 Running dot for graph 28/84 Running dot for graph 29/84 Running dot for graph 30/84 Running dot for graph 31/84 Running dot for graph 32/84 Running dot for graph 33/84 Running dot for graph 34/84 Running dot for graph 35/84 Running dot for graph 36/84 Running dot for graph 37/84 Running dot for graph 38/84 Running dot for graph 39/84 Running dot for graph 40/84 Running dot for graph 41/84 Running dot for graph 42/84 Running dot for graph 43/84 Running dot for graph 44/84 Running dot for graph 45/84 Running dot for graph 46/84 Running dot for graph 47/84 Running dot for graph 48/84 Running dot for graph 49/84 Running dot for graph 50/84 Running dot for graph 51/84 Running dot for graph 52/84 Running dot for graph 53/84 Running dot for graph 54/84 Running dot for graph 55/84 Running dot for graph 56/84 Running dot for graph 57/84 Running dot for graph 58/84 Running dot for graph 59/84 Running dot for graph 60/84 Running dot for graph 61/84 Running dot for graph 62/84 Running dot for graph 63/84 Running dot for graph 64/84 Running dot for graph 65/84 Running dot for graph 66/84 Running dot for graph 67/84 Running dot for graph 68/84 Running dot for graph 69/84 Running dot for graph 70/84 Running dot for graph 71/84 Running dot for graph 72/84 Running dot for graph 73/84 Running dot for graph 74/84 Running dot for graph 75/84 Running dot for graph 76/84 Running dot for graph 77/84 Running dot for graph 78/84 Running dot for graph 79/84 Running dot for graph 80/84 Running dot for graph 81/84 Running dot for graph 82/84 Running dot for graph 83/84 Running dot for graph 84/84 Patching output file 1/57 lookup cache used 2285/65536 hits=43969 misses=2419 finished... make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Built target doc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 55%] Generating pdf documentation make[3]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/latex' This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-05-07> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array-2016-10-06.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) All fixes are now in the LaTeX kernel. (fixltx2e) See the latexrelease package for details. ) (./doxygen.sty (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty)) (./longtable_doxygen.sty) (./tabu_doxygen.sty (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/hanging/hanging.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifpdf.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjustbox.sty (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex))) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/trimclip.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/collectbox/collectbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/tc-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/stackengine/stackengine.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/listofitems/listofitems.sty (/usr/share/texlive/texmf-dist/tex/generic/listofitems/listofitems.tex))) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/generic/alphalph/alphalph.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/wasysym.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/helvet.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/courier.sty) (/usr/share/texlive/texmf-dist/tex/latex/sectsty/sectsty.sty LaTeX Warning: Command \underbar has changed. Check if current package is valid. LaTeX Warning: Command \underline has changed. Check if current package is valid. ) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/tocloft/tocloft.sty) Writing index file refman.idx (/usr/share/texlive/texmf-dist/tex/latex/newunicodechar/newunicodechar.sty) Package newunicodechar Warning: Redefining Unicode character on input line 116. Package newunicodechar Warning: Redefining Unicode character on input line 117. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/backref.sty (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty) (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoc/etoc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file refman.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) No file refman.toc. [1{/usr/share/texlive/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2] Chapter 1. (./index.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) [3] [4] Chapter 2. (./bug.tex [5] [6]) [7] [8] Chapter 3. (./deprecated.tex) [9] [10] Chapter 4. (./modules.tex LaTeX Warning: Reference `group___header' on page 11 undefined on input line 3. LaTeX Warning: Reference `group___vcsm' on page 11 undefined on input line 4. LaTeX Warning: Reference `group___vfetk' on page 11 undefined on input line 5. LaTeX Warning: Reference `group___vpee' on page 11 undefined on input line 6. LaTeX Warning: Reference `group___a_p_o_lparm' on page 11 undefined on input li ne 7. LaTeX Warning: Reference `group___b_e_mparm' on page 11 undefined on input line 8. LaTeX Warning: Reference `group___f_e_mparm' on page 11 undefined on input line 9. LaTeX Warning: Reference `group___g_e_o_f_l_o_wparm' on page 11 undefined on in put line 10. LaTeX Warning: Reference `group___m_gparm' on page 11 undefined on input line 1 1. LaTeX Warning: Reference `group___n_osh' on page 11 undefined on input line 12. LaTeX Warning: Reference `group___p_b_a_mparm' on page 11 undefined on input li ne 13. LaTeX Warning: Reference `group___p_b_eparm' on page 11 undefined on input line 14. LaTeX Warning: Reference `group___p_b_s_a_mparm' on page 11 undefined on input line 15. LaTeX Warning: Reference `group___vacc' on page 11 undefined on input line 16. LaTeX Warning: Reference `group___valist' on page 11 undefined on input line 17 . LaTeX Warning: Reference `group___vatom' on page 11 undefined on input line 18. LaTeX Warning: Reference `group___vcap' on page 11 undefined on input line 19. LaTeX Warning: Reference `group___vclist' on page 11 undefined on input line 20 . LaTeX Warning: Reference `group___vgreen' on page 11 undefined on input line 21 . LaTeX Warning: Reference `group___vhal' on page 11 undefined on input line 22. LaTeX Warning: Reference `group___vmatrix' on page 11 undefined on input line 2 3. LaTeX Warning: Reference `group___vparam' on page 11 undefined on input line 24 . LaTeX Warning: Reference `group___vpbe' on page 11 undefined on input line 25. LaTeX Warning: Reference `group___vstring' on page 11 undefined on input line 2 6. LaTeX Warning: Reference `group___vunit' on page 11 undefined on input line 27. LaTeX Warning: Reference `group___vgrid' on page 11 undefined on input line 28. LaTeX Warning: Reference `group___vmgrid' on page 11 undefined on input line 29 . LaTeX Warning: Reference `group___vopot' on page 11 undefined on input line 30. LaTeX Warning: Reference `group___vpmg' on page 11 undefined on input line 31. LaTeX Warning: Reference `group___vpmgp' on page 11 undefined on input line 32. LaTeX Warning: Reference `group___p_m_g_c' on page 11 undefined on input line 3 3. LaTeX Warning: Reference `group___frontend' on page 11 undefined on input line 34. ) [11] [12] Chapter 5. (./annotated.tex LaTeX Warning: Reference `struct_atom_force' on page 13 undefined on input line 3. LaTeX Warning: Reference `structs_a_p_o_lparm' on page 13 undefined on input li ne 4. LaTeX Warning: Reference `structs_b_e_mparm' on page 13 undefined on input line 5. LaTeX Warning: Reference `structs_f_e_mparm' on page 13 undefined on input line 6. LaTeX Warning: Reference `structs_g_e_o_f_l_o_wparm' on page 13 undefined on in put line 7. LaTeX Warning: Reference `structs_m_gparm' on page 13 undefined on input line 8 . LaTeX Warning: Reference `structs_n_osh' on page 13 undefined on input line 9. LaTeX Warning: Reference `structs_n_osh__calc' on page 13 undefined on input li ne 10. LaTeX Warning: Reference `structs_p_b_a_mparm' on page 13 undefined on input li ne 11. LaTeX Warning: Reference `structs_p_b_eparm' on page 13 undefined on input line 12. LaTeX Warning: Reference `structs_p_b_s_a_mparm' on page 13 undefined on input line 13. LaTeX Warning: Reference `structs_vacc' on page 13 undefined on input line 14. LaTeX Warning: Reference `structs_vacc_surf' on page 13 undefined on input line 15. LaTeX Warning: Reference `structs_valist' on page 13 undefined on input line 16 . LaTeX Warning: Reference `structs_vatom' on page 13 undefined on input line 17. LaTeX Warning: Reference `structs_vclist' on page 13 undefined on input line 18 . LaTeX Warning: Reference `structs_vclist_cell' on page 13 undefined on input li ne 19. LaTeX Warning: Reference `structs_vcsm' on page 13 undefined on input line 20. LaTeX Warning: Reference `structs_vfetk' on page 13 undefined on input line 21. [13] LaTeX Warning: Reference `structs_vfetk___local_var' on page 14 undefined on in put line 22. LaTeX Warning: Reference `structs_vgreen' on page 14 undefined on input line 23 . LaTeX Warning: Reference `structs_vgrid' on page 14 undefined on input line 24. LaTeX Warning: Reference `structs_vmgrid' on page 14 undefined on input line 25 . LaTeX Warning: Reference `structs_vopot' on page 14 undefined on input line 26. LaTeX Warning: Reference `structs_vparam___atom_data' on page 14 undefined on i nput line 27. LaTeX Warning: Reference `structs_vpbe' on page 14 undefined on input line 28. LaTeX Warning: Reference `structs_vpee' on page 14 undefined on input line 29. LaTeX Warning: Reference `structs_vpmg' on page 14 undefined on input line 30. LaTeX Warning: Reference `structs_vpmgp' on page 14 undefined on input line 31. LaTeX Warning: Reference `struct_vparam' on page 14 undefined on input line 32. LaTeX Warning: Reference `struct_vparam___res_data' on page 14 undefined on inp ut line 33. ) [14] Chapter 6. (./files.tex LaTeX Warning: Reference `mainpage_8h_source' on page 15 undefined on input lin e 3. LaTeX Warning: Reference `apbs_8h' on page 15 undefined on input line 4. LaTeX Warning: Reference `main_8c' on page 15 undefined on input line 5. LaTeX Warning: Reference `routines_8c' on page 15 undefined on input line 6. LaTeX Warning: Reference `routines_8h' on page 15 undefined on input line 7. LaTeX Warning: Reference `vcsm_8c' on page 15 undefined on input line 8. LaTeX Warning: Reference `vcsm_8h' on page 15 undefined on input line 9. LaTeX Warning: Reference `vfetk_8c' on page 15 undefined on input line 10. LaTeX Warning: Reference `vfetk_8h' on page 15 undefined on input line 11. LaTeX Warning: Reference `vpee_8c' on page 15 undefined on input line 12. LaTeX Warning: Reference `vpee_8h' on page 15 undefined on input line 13. LaTeX Warning: Reference `apolparm_8c' on page 15 undefined on input line 14. 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LaTeX Warning: Reference `smoothd_8h_source' on page 18 undefined on input line 98. ) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.1 on input line 102. Overfull \vbox (13.81569pt too high) has occurred while \output is active [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.2 on input line 130. Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.3 on input line 164. 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Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.97 on input line 355. [75] Underfull \hbox (badness 10000) detected at line 370 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.98 on input line 377. ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.99 on input line 106. [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.100 on input line 131. Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.101 on input line 158. [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.102 on input line 180. Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.103 on input line 207. Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.104 on input line 232. [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.105 on input line 254. Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.106 on input line 280. Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Package longtable Warning: Column widths have changed (longtable) in table 7.107 on input line 175. Package longtable Warning: Column widths have changed (longtable) in table 7.108 on input line 203. Underfull \hbox (badness 10000) detected at line 221 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.109 on input line 232. [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.110 on input line 261. Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.111 on input line 286. Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.112 on input line 313. Underfull \hbox (badness 10000) detected at line 328 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.113 on input line 335. Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.114 on input line 362. Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.115 on input line 387. Underfull \hbox (badness 10000) detected at line 402 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.116 on input line 409. Underfull \hbox (badness 10000) detected at line 424 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.117 on input line 431. [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.118 on input line 456. Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.119 on input line 481. Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.120 on input line 506. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.121 on input line 531. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.122 on input line 556. Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.123 on input line 581. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.124 on input line 606. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.125 on input line 631. [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.126 on input line 660. Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.127 on input line 687. [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.128 on input line 711. Underfull \hbox (badness 10000) detected at line 726 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.129 on input line 735. ) (./group___n_osh.tex [91] [92] [93] [94] Package longtable Warning: Column widths have changed (longtable) in table 7.130 on input line 337. [95] Package longtable Warning: Column widths have changed (longtable) in table 7.131 on input line 365. Package longtable Warning: Column widths have changed (longtable) in table 7.132 on input line 389. Package longtable Warning: Column widths have changed (longtable) in table 7.133 on input line 429. [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.134 on input line 456. Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.135 on input line 483. Underfull \hbox (badness 10000) detected at line 498 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.136 on input line 505. [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.137 on input line 530. Underfull \hbox (badness 10000) detected at line 545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.138 on input line 554. Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.139 on input line 583. Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.140 on input line 608. Underfull \hbox (badness 10000) detected at line 623 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.141 on input line 630. [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.142 on input line 654. Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.143 on input line 684. Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.144 on input line 714. Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.145 on input line 741. Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.146 on input line 768. Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.147 on input line 795. Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.148 on input line 822. Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.149 on input line 849. Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.150 on input line 876. Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Package longtable Warning: Column widths have changed (longtable) in table 7.151 on input line 903. Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.152 on input line 930. Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.153 on input line 957. [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.154 on input line 984. Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.155 on input line 1011. Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.156 on input line 1041. Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.157 on input line 1073. Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.158 on input line 1105. Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.159 on input line 1138. Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.160 on input line 1173. Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Package longtable Warning: Column widths have changed (longtable) in table 7.161 on input line 1206. Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.162 on input line 1239. Underfull \hbox (badness 10000) detected at line 1240 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.163 on input line 1249. [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.164 on input line 1276. Underfull \hbox (badness 10000) detected at line 1277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.165 on input line 1286. ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.166 on input line 154. Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.167 on input line 179. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.168 on input line 206. [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.169 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.170 on input line 255. Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.171 on input line 280. [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.172 on input line 302. Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.173 on input line 326. Underfull \hbox (badness 10000) detected at line 341 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.174 on input line 350. [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.175 on input line 374. Underfull \hbox (badness 10000) detected at line 389 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.176 on input line 398. Underfull \hbox (badness 10000) detected at line 413 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.177 on input line 422. [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.178 on input line 446. Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.179 on input line 470. Underfull \hbox (badness 10000) detected at line 485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.180 on input line 494. Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.181 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.182 on input line 542. Underfull \hbox (badness 10000) detected at line 557 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.183 on input line 566. Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.184 on input line 592. Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.185 on input line 619. [119] Underfull \hbox (badness 10000) detected at line 634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.186 on input line 643. ) (./group___p_b_eparm.tex [120] [121] Package longtable Warning: Column widths have changed (longtable) in table 7.187 on input line 163. Package longtable Warning: Column widths have changed (longtable) in table 7.188 on input line 191. [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.189 on input line 219. Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.190 on input line 243. Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.191 on input line 288. Underfull \hbox (badness 10000) detected at line 303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.192 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.193 on input line 332. [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.194 on input line 359. Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.195 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Package longtable Warning: Column widths have changed (longtable) in table 7.196 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.197 on input line 442. ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.198 on input line 138. [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.199 on input line 163. Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.200 on input line 190. Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.201 on input line 212. Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.202 on input line 239. Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.203 on input line 264. Underfull \hbox (badness 10000) detected at line 279 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.204 on input line 286. [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.205 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.206 on input line 334. Underfull \hbox (badness 10000) detected at line 349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.207 on input line 358. Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.208 on input line 382. Underfull \hbox (badness 10000) detected at line 397 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.209 on input line 408. Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.210 on input line 435. ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.211 on input line 164. Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.212 on input line 192. [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.213 on input line 224. Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.214 on input line 253. [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.215 on input line 282. Underfull \hbox (badness 10000) detected at line 283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.216 on input line 290. Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.217 on input line 319. [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.218 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.219 on input line 372. [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.220 on input line 394. Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.221 on input line 430. [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.222 on input line 461. Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.223 on input line 482. Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.224 on input line 515. Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.225 on input line 545. [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.226 on input line 578. Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.227 on input line 613. [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.228 on input line 643. Underfull \hbox (badness 10000) detected at line 660 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.229 on input line 677. [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.230 on input line 709. Underfull \hbox (badness 10000) detected at line 724 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.231 on input line 741. [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.232 on input line 775. Underfull \hbox (badness 10000) detected at line 790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.233 on input line 805. Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.234 on input line 837. Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.235 on input line 867. [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.236 on input line 901. Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.237 on input line 930. Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.238 on input line 957. Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.239 on input line 992. [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.240 on input line 1025. Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Package longtable Warning: Column widths have changed (longtable) in table 7.241 on input line 1054. Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.242 on input line 1085. Underfull \hbox (badness 10000) detected at line 1100 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.243 on input line 1107. [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.244 on input line 1129. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.245 on input line 1161. ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.246 on input line 121. Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Package longtable Warning: Column widths have changed (longtable) in table 7.247 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.248 on input line 165. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.249 on input line 192. [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.250 on input line 217. Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.251 on input line 242. Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.252 on input line 267. [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.253 on input line 292. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.254 on input line 317. Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.255 on input line 362. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.256 on input line 394. [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.257 on input line 428. Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159] Package longtable Warning: Column widths have changed (longtable) in table 7.258 on input line 462. ) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.259 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.260 on input line 167. [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.261 on input line 209. Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.262 on input line 234. [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.263 on input line 256. Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.264 on input line 278. Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.265 on input line 305. [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.266 on input line 327. Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.267 on input line 352. Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.268 on input line 377. [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.269 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.270 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.271 on input line 454. Underfull \hbox (badness 10000) detected at line 469 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.272 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.273 on input line 503. [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.274 on input line 527. Underfull \hbox (badness 10000) detected at line 542 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.275 on input line 551. Underfull \hbox (badness 10000) detected at line 566 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.276 on input line 575. [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.277 on input line 599. Underfull \hbox (badness 10000) detected at line 614 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.278 on input line 623. Underfull \hbox (badness 10000) detected at line 638 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.279 on input line 647. [169] Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.280 on input line 671. ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.281 on input line 101. Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.282 on input line 134. Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.283 on input line 167. ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.284 on input line 138. Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.285 on input line 176. [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.286 on input line 213. Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Package longtable Warning: Column widths have changed (longtable) in table 7.287 on input line 235. Underfull \hbox (badness 10000) detected at line 250 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.288 on input line 257. Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.289 on input line 284. [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.290 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.291 on input line 334. Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.292 on input line 359. [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.293 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.294 on input line 408. Underfull \hbox (badness 10000) detected at line 423 [][][] [179] Package longtable Warning: Column widths have changed (longtable) in table 7.295 on input line 430. ) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.296 on input line 158. Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.297 on input line 195. Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.298 on input line 238. Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.299 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.300 on input line 306. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Package longtable Warning: Column widths have changed (longtable) in table 7.301 on input line 333. Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.302 on input line 358. Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.303 on input line 380. [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.304 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.305 on input line 448. [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.306 on input line 499. Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.307 on input line 524. Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.308 on input line 794. Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.309 on input line 825. Underfull \hbox (badness 10000) detected at line 840 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.310 on input line 860. Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.311 on input line 907. [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. Package longtable Warning: Column widths have changed (longtable) in table 7.312 on input line 986. [199] Package longtable Warning: Column widths have changed (longtable) in table 7.313 on input line 1014. Package longtable Warning: Column widths have changed (longtable) in table 7.314 on input line 1060. Package longtable Warning: Column widths have changed (longtable) in table 7.315 on input line 1084. Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.316 on input line 1115. Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.317 on input line 1175. ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.318 on input line 161. Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.319 on input line 188. Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.320 on input line 215. [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.321 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.322 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.323 on input line 306. Underfull \hbox (badness 10000) detected at line 321 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.324 on input line 328. Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Package longtable Warning: Column widths have changed (longtable) in table 7.325 on input line 370. Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.326 on input line 395. Underfull \hbox (badness 10000) detected at line 410 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.327 on input line 417. [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.328 on input line 443. Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.329 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.330 on input line 507. Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.331 on input line 540. Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.332 on input line 584. Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.333 on input line 611. [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.334 on input line 633. Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.335 on input line 660. Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.336 on input line 685. Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.337 on input line 707. ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Package longtable Warning: Column widths have changed (longtable) in table 7.338 on input line 171. Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.339 on input line 232. Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.340 on input line 254. [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.341 on input line 276. Underfull \hbox (badness 10000) detected at line 291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.342 on input line 298. Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Package longtable Warning: Column widths have changed (longtable) in table 7.343 on input line 332. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.344 on input line 357. Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.345 on input line 382. Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.346 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.347 on input line 435. Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Package longtable Warning: Column widths have changed (longtable) in table 7.348 on input line 460. Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.349 on input line 485. Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.350 on input line 510. [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.351 on input line 532. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.352 on input line 557. Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.353 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.354 on input line 607. Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.355 on input line 632. Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.356 on input line 657. [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.357 on input line 682. Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.358 on input line 707. Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.359 on input line 732. Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.360 on input line 757. Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.361 on input line 782. Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.362 on input line 807. Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.363 on input line 832. Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.364 on input line 857. [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.365 on input line 882. Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.366 on input line 907. Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.367 on input line 932. Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Package longtable Warning: Column widths have changed (longtable) in table 7.368 on input line 49. Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.369 on input line 79. Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.370 on input line 116. ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.371 on input line 150. Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.372 on input line 195. Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Package longtable Warning: Column widths have changed (longtable) in table 7.373 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.374 on input line 253. Underfull \hbox (badness 10000) detected at line 268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.375 on input line 275. [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.376 on input line 301. Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.377 on input line 326. Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Package longtable Warning: Column widths have changed (longtable) in table 7.378 on input line 351. Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.379 on input line 376. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.380 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.381 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.382 on input line 452. Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.383 on input line 488. Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.384 on input line 527. Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.385 on input line 560. Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.386 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.387 on input line 611. Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.388 on input line 648. [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.389 on input line 682. Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245] Package longtable Warning: Column widths have changed (longtable) in table 7.390 on input line 721. ) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Package longtable Warning: Column widths have changed (longtable) in table 7.391 on input line 114. Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.392 on input line 159. Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.393 on input line 192. Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.394 on input line 217. [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.395 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.396 on input line 263. Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.397 on input line 286. Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.398 on input line 311. Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.399 on input line 340. Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.400 on input line 88. Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.401 on input line 119. Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.402 on input line 152. Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.403 on input line 177. [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.404 on input line 199. Underfull \hbox (badness 10000) detected at line 214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.405 on input line 225. Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.406 on input line 254. [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.407 on input line 171. [259] Underfull \hbox (badness 10000) detected at line 186 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.408 on input line 219. [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.412 on input line 401. Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.413 on input line 443. Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.414 on input line 473. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Package longtable Warning: Column widths have changed (longtable) in table 7.415 on input line 505. Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.416 on input line 535. Underfull \hbox (badness 10000) detected at line 546 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.417 on input line 561. [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.418 on input line 583. Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Package longtable Warning: Column widths have changed (longtable) in table 7.419 on input line 619. Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.420 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.421 on input line 675. [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.422 on input line 697. Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.423 on input line 727. [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.424 on input line 753. Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.425 on input line 784. [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.426 on input line 841. [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.427 on input line 879. Underfull \hbox (badness 10000) detected at line 894 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.428 on input line 909. [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.429 on input line 941. Underfull \hbox (badness 10000) detected at line 956 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.430 on input line 971. [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.431 on input line 997. Underfull \hbox (badness 10000) detected at line 1008 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.432 on input line 1019. [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.433 on input line 1040. Underfull \hbox (badness 10000) detected at line 1055 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.434 on input line 1076. [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.435 on input line 1108. [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.436 on input line 1140. Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.437 on input line 1175. [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.438 on input line 1211. Underfull \hbox (badness 10000) detected at line 1226 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.439 on input line 1241. [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.440 on input line 1269. Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.441 on input line 1292. Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.442 on input line 1316. Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Package longtable Warning: Column widths have changed (longtable) in table 7.443 on input line 1358. Underfull \hbox (badness 10000) detected at line 1373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.444 on input line 1386. Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.445 on input line 1411. [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.446 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.447 on input line 1461. ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.448 on input line 85. Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.449 on input line 112. Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Package longtable Warning: Column widths have changed (longtable) in table 7.450 on input line 137. Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.451 on input line 159. Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.452 on input line 193. [285] Underfull \hbox (badness 10000) detected at line 208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.453 on input line 215. ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.454 on input line 293. [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.455 on input line 324. Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.457 on input line 631. [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.458 on input line 704. [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.459 on input line 757. [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1567. [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1713. Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.467 on input line 1751. [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.468 on input line 1788. Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Package longtable Warning: Column widths have changed (longtable) in table 7.469 on input line 1825. Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.470 on input line 1862. [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2016. [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.472 on input line 2053. [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.473 on input line 2188. [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.474 on input line 2227. [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2266. Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.476 on input line 2297. [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2486. [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2680. [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2729. Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2888. Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.481 on input line 2929. [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3029. [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.483 on input line 3170. [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3325. [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3416. [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3525. Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.487 on input line 3568. [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3772. [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3873. [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.490 on input line 3955. Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.491 on input line 3984. [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.492 on input line 4017. [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4177. [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4273. Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4366. [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.496 on input line 4409. Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Package longtable Warning: Column widths have changed (longtable) in table 7.497 on input line 4454. Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4515. [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4679. [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.500 on input line 4710. [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.501 on input line 4751. Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4913. [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.503 on input line 4948. Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.504 on input line 5084. [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.505 on input line 5120. Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.506 on input line 5153. [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.507 on input line 5186. Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.508 on input line 5217. Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.509 on input line 5248. [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.510 on input line 5281. ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.511 on input line 196. Underfull \hbox (badness 10000) detected at line 211 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.512 on input line 232. [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.513 on input line 260. Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.514 on input line 296. [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.515 on input line 336. [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.516 on input line 372. Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] Package longtable Warning: Column widths have changed (longtable) in table 7.517 on input line 480. [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.518 on input line 557. [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.519 on input line 610. [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.520 on input line 634. Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.521 on input line 662. Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.522 on input line 705. Underfull \hbox (badness 10000) detected at line 720 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.523 on input line 733. [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.524 on input line 757. Underfull \hbox (badness 10000) detected at line 772 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.525 on input line 781. Underfull \hbox (badness 10000) detected at line 792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.526 on input line 803. [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.527 on input line 827. Underfull \hbox (badness 10000) detected at line 842 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.528 on input line 851. Underfull \hbox (badness 10000) detected at line 866 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.529 on input line 875. [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.530 on input line 908. Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.531 on input line 938. [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.532 on input line 970. Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.533 on input line 995. [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.534 on input line 1020. Underfull \hbox (badness 10000) detected at line 1035 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.535 on input line 1044. Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.536 on input line 1076. Underfull \hbox (badness 10000) detected at line 1091 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.537 on input line 1104. Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.538 on input line 1133. Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.539 on input line 1151. Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.540 on input line 1179. Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.541 on input line 1213. Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.542 on input line 1244. [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.543 on input line 1273. Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.544 on input line 1304. [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.545 on input line 1333. Underfull \hbox (badness 10000) detected at line 1348 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.546 on input line 1362. [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.547 on input line 1393. Underfull \hbox (badness 10000) detected at line 1408 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.548 on input line 1417. Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.549 on input line 1439. [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.550 on input line 1467. Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.551 on input line 1496. Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.552 on input line 1527. Underfull \hbox (badness 10000) detected at line 1528 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.553 on input line 1547. Underfull \hbox (badness 10000) detected at line 1562 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.554 on input line 1573. [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.555 on input line 1621. [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.556 on input line 1649. Underfull \hbox (badness 10000) detected at line 1650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.557 on input line 1673. Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Package longtable Warning: Column widths have changed (longtable) in table 7.558 on input line 1715. Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.559 on input line 1746. Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.560 on input line 1791. Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.561 on input line 1822. [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.1 on input line 124. [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.2 on input line 187. Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.3 on input line 218. Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.4 on input line 182. [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.5 on input line 172. ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.6 on input line 313. [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 388. Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 438. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 463. [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 488. Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 513. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.13 on input line 855. Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Package longtable Warning: Column widths have changed (longtable) in table 9.14 on input line 885. Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Package longtable Warning: Column widths have changed (longtable) in table 9.15 on input line 927. Underfull \hbox (badness 10000) detected at line 942 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.16 on input line 949. Underfull \hbox (badness 10000) detected at line 964 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.17 on input line 971. [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.18 on input line 1016. Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.19 on input line 1041. [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.20 on input line 1066. Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.21 on input line 1125. Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.22 on input line 1152. ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.23 on input line 442. [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 492. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 517. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 542. [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 567. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.30 on input line 930. [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.31 on input line 960. Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Package longtable Warning: Column widths have changed (longtable) in table 9.32 on input line 982. Underfull \hbox (badness 10000) detected at line 997 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.33 on input line 1004. Underfull \hbox (badness 10000) detected at line 1019 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.34 on input line 1026. [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.35 on input line 1071. Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.36 on input line 1096. [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.37 on input line 1121. 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[1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox 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Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1406 pages, 5228398 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2021] (kpathsea + Thai support). Scanning input file refman.idx.......done (3686 entries accepted, 0 rejected). Sorting entries....................................done (49276 comparisons). 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(./index.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) [3] [4] Chapter 2. (./bug.tex [5] [6]) [7] [8] Chapter 3. (./deprecated.tex) [9] [10] Chapter 4. (./modules.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] Overfull \vbox (13.81569pt too high) has occurred while \output is active [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Overfull \vbox (22.52646pt too high) has occurred while \output is active [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] [24] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [25] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Overfull \vbox (8.04509pt too high) has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1567. [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1713. Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2016. [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2266. Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2486. [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2680. [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2729. Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2888. Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3029. [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3325. [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3416. [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3525. Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3772. [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3873. [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4177. [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4273. Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4366. [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4515. [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4679. [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4913. [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 388. Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 438. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 463. [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 488. Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 513. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 492. Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 517. Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 542. [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 567. Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 84--85 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1325] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./routines_8c_source.tex [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int 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Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1511 pages, 5646963 bytes). Transcript written on refman.log. Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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\hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] [24] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [25] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Overfull \vbox (8.04509pt too high) has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Underfull \hbox (badness 10000) detected at line 324 [][][] [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] 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[1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1396] Underfull \hbox (badness 2495) in paragraph at lines 112--113 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1397] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] [1398]) (./routines_8h_source.tex [1399] [1400] [1401] [1402]) [1403] [1404] (./refman.ind [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] 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This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-05-07> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array-2016-10-06.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/fixltx2e.sty Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) All fixes are now in the LaTeX kernel. 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has occurred while \output is active [26]) (./group___vfetk.tex [27] [28] [29] [30] [31] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [32] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Overfull \vbox (16.64539pt too high) has occurred while \output is active [33] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Overfull \vbox (29.02182pt too high) has occurred while \output is active [34] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 609 [][][] [35] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] [36] Underfull \hbox (badness 10000) detected at line 677 [][][] Underfull \hbox (badness 10000) detected at line 707 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] [37] Underfull \hbox (badness 10000) detected at line 741 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [38] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] [39] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [40] Underfull \hbox (badness 10000) detected at line 930 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [41] Underfull \hbox (badness 10000) detected at line 1005 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [42] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [43] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] Underfull \hbox (badness 10000) detected at line 1155 [][][] [44] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1188 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1213 [][][] [45] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] [46] Underfull \hbox (badness 10000) detected at line 1304 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1333 [][][] [47] Underfull \hbox (badness 10000) detected at line 1361 [][][] Underfull \hbox (badness 10000) detected at line 1391 [][][] [48] Underfull \hbox (badness 10000) detected at line 1425 [][][] Underfull \hbox (badness 10000) detected at line 1428 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] [49] Underfull \hbox (badness 10000) detected at line 1457 [][][] Underfull \hbox (badness 10000) detected at line 1483 [][][] Underfull \hbox (badness 10000) detected at line 1486 [][][] [50] Underfull \hbox (badness 10000) detected at line 1520 [][][] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1551 [][][] [51] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] [52] Underfull \hbox (badness 10000) detected at line 1671 [][][] [53] Underfull \hbox (badness 10000) detected at line 1705 [][][] Underfull \hbox (badness 10000) detected at line 1708 [][][] [54] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1761 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] Underfull \hbox (badness 10000) detected at line 1788 [][][] Underfull \hbox (badness 10000) detected at line 1791 [][][] [55] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1816 [][][] Underfull \hbox (badness 10000) detected at line 1819 [][][] Underfull \hbox (badness 10000) detected at line 1841 [][][] [56] Underfull \hbox (badness 10000) detected at line 1867 [][][] Underfull \hbox (badness 10000) detected at line 1887 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] ) (./group___vpee.tex [57] [58] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [59] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [60] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] [61] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [62] [63] Overfull \vbox (4.40634pt too high) has occurred while \output is active [64] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 253 [][][] Overfull \vbox (19.76988pt too high) has occurred while \output is active [65] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] [66] Underfull \hbox (badness 10000) detected at line 344 [][][] ) (./group___b_e_mparm.tex [67] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [68] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Overfull \vbox (20.2591pt too high) has occurred while \output is active [69] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [70] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [71] Underfull \hbox (badness 10000) detected at line 127 [][][] [72] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Overfull \vbox (13.4703pt too high) has occurred while \output is active [73] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] [74] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] [75] Underfull \hbox (badness 10000) detected at line 370 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [76] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [77] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] [78] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] [79] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [80] [81] [82] Underfull \hbox (badness 10000) detected at line 221 [][][] [83] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [84] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Overfull \vbox (3.48517pt too high) has occurred while \output is active [85] Underfull \hbox (badness 10000) detected at line 363 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [86] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [87] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 549 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [88] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] [89] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] [90] Underfull \hbox (badness 10000) detected at line 702 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] ) (./group___n_osh.tex [91] [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] [97] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 523 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 555 [][][] [98] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 601 [][][] Underfull \hbox (badness 10000) detected at line 623 [][][] [99] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 685 [][][] Underfull \hbox (badness 10000) detected at line 688 [][][] [100] Underfull \hbox (badness 10000) detected at line 705 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Overfull \vbox (15.8999pt too high) has occurred while \output is active [101] Underfull \hbox (badness 10000) detected at line 769 [][][] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 796 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 823 [][][] [102] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 877 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [103] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 931 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [104] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] [105] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1032 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1074 [][][] [106] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1094 [][][] Underfull \hbox (badness 10000) detected at line 1106 [][][] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] Underfull \hbox (badness 10000) detected at line 1139 [][][] [107] Underfull \hbox (badness 10000) detected at line 1142 [][][] Underfull \hbox (badness 10000) detected at line 1159 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] Underfull \hbox (badness 10000) detected at line 1174 [][][] Underfull \hbox (badness 10000) detected at line 1177 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] [108] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Underfull \hbox (badness 10000) detected at line 1227 [][][] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1240 [][][] [109] Underfull \hbox (badness 10000) detected at line 1264 [][][] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1277 [][][] ) (./group___p_b_a_mparm.tex [110] [111] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Overfull \vbox (0.52336pt too high) has occurred while \output is active [112] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [113] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] [114] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [115] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [116] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] Overfull \vbox (17.70645pt too high) has occurred while \output is active [117] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Overfull \vbox (17.5984pt too high) has occurred while \output is active [118] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [119] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [120] [121] [122] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] [123] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [124] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] [125] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] ) (./group___p_b_s_a_mparm.tex [126] [127] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [128] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [129] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] [130] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Overfull \vbox (18.2195pt too high) has occurred while \output is active [131] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] [132] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [133] [134] [135] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [136] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [137] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [138] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] [139] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] [140] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] [141] Underfull \hbox (badness 10000) detected at line 502 [][][] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] [142] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] [143] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 660 [][][] [144] Underfull \hbox (badness 10000) detected at line 692 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [145] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 790 [][][] Overfull \vbox (2.17566pt too high) has occurred while \output is active [146] Underfull \hbox (badness 10000) detected at line 820 [][][] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [147] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Overfull \vbox (7.9985pt too high) has occurred while \output is active [148] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [149] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] [150] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] [151] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] ) (./group___valist.tex [152] [153] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] [154] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [155] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [156] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [157] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [158] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] [159]) (./group___vatom.tex [160] Underfull \hbox (badness 10000) detected at line 97 [][][] [161] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] [162] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] [163] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] [164] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [165] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] [166] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] [167] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] [168] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] [169] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [170] Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Overfull \vbox (22.8879pt too high) has occurred while \output is active [171] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [172] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [173] [174] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [175] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] [176] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [177] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] [178] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [179]) (./group___vgreen.tex [180] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [181] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] [182] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] [183] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [184] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] [185] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] [186] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] [187] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [188] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [189] [190] [191] [192] Underfull \hbox (badness 10000) detected at line 390 [][][] [193] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 438 [][][] Underfull \hbox (badness 10000) detected at line 455 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [194] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [195] [196] Underfull \hbox (badness 10000) detected at line 762 [][][] Overfull \vbox (16.5709pt too high) has occurred while \output is active [197] Underfull \hbox (badness 10000) detected at line 809 [][][] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] [198] Underfull \hbox (badness 10000) detected at line 922 [][][] LaTeX Warning: Command \r invalid in math mode on input line 58. [199] Underfull \hbox (badness 10000) detected at line 1099 [][][] [200] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1130 [][][] Underfull \hbox (badness 10000) detected at line 1133 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] ) (./group___vmatrix.tex [201]) (./group___vparam.tex [202] [203] Underfull \hbox (badness 10000) detected at line 152 [][][] Overfull \vbox (16.48396pt too high) has occurred while \output is active [204] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] [205] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [206] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [207] Underfull \hbox (badness 10000) detected at line 371 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 410 [][][] [208] Underfull \hbox (badness 10000) detected at line 432 [][][] Underfull \hbox (badness 10000) detected at line 444 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] [209] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] [210] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [211] Underfull \hbox (badness 10000) detected at line 626 [][][] Underfull \hbox (badness 10000) detected at line 634 [][][] Underfull \hbox (badness 10000) detected at line 651 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [212] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] ) (./group___vpbe.tex [213] [214] [215] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. LaTeX Warning: Command \r invalid in math mode on input line 133. Underfull \hbox (badness 10000) detected at line 136 [][][] [216] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. LaTeX Warning: Command \r invalid in math mode on input line 190. [217] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [218] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] [219] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [220] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [221] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [222] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [223] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] [224] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [225] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] [226] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] Underfull \hbox (badness 10000) detected at line 850 [][][] [227] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [228] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex Underfull \hbox (badness 10000) detected at line 42 [][][] [229] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [230] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [231] LaTeX Warning: Command \r invalid in math mode on input line 39. [232] LaTeX Warning: Command \r invalid in math mode on input line 142. [233]) (./group___vgrid.tex [234] [235] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [236] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [237] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] [238] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] [239] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [240] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] [241] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Overfull \vbox (18.5518pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] [243] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [244] Underfull \hbox (badness 10000) detected at line 663 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [245]) (./group___vmgrid.tex [246] Underfull \hbox (badness 10000) detected at line 105 [][][] [247] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] [248] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [249] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] [250] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [251] [252] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [253] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [254] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [255] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [256] [257] [258] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [259] Underfull \hbox (badness 10000) detected at line 186 [][][] [260] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [261] Underfull \hbox (badness 10000) detected at line 324 [][][] [262] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] [263] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Overfull \vbox (0.60114pt too high) has occurred while \output is active [264] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [265] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [266] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [267] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [268] Underfull \hbox (badness 10000) detected at line 690 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] [269] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] [270] Underfull \hbox (badness 10000) detected at line 799 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [271] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [272] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] [273] Underfull \hbox (badness 10000) detected at line 982 [][][] Underfull \hbox (badness 10000) detected at line 1008 [][][] [274] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Underfull \hbox (badness 10000) detected at line 1055 [][][] [275] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] [276] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] [277] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Underfull \hbox (badness 10000) detected at line 1226 [][][] [278] Underfull \hbox (badness 10000) detected at line 1252 [][][] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Overfull \vbox (17.89487pt too high) has occurred while \output is active [279] Underfull \hbox (badness 10000) detected at line 1303 [][][] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] [280] Underfull \hbox (badness 10000) detected at line 1373 [][][] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] [281] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [282] Underfull \hbox (badness 10000) detected at line 45 [][][] [283] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [284] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [285] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [286] [287] [288] [289] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [290] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [291] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [292] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] [293] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] Underfull \hbox (badness 10000) detected at line 439 [][][] [295] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [296] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [297] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [298] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [299] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [300] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [301] [302] Underfull \hbox (badness 10000) detected at line 907 [][][] [303] Underfull \hbox (badness 10000) detected at line 910 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [306] [307] [308] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [309] [310] Underfull \hbox (badness 10000) detected at line 1382 [][][] [311] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [312] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1499 [][][] Underfull \hbox (badness 10000) detected at line 1502 [][][] [314] Underfull \hbox (badness 10000) detected at line 1582 [][][] Underfull \hbox (badness 10000) detected at line 1585 [][][] Underfull \hbox (badness 10000) detected at line 1588 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1598--1598 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [315] Underfull \hbox (badness 10000) detected at line 1635 [][][] Underfull \hbox (badness 10000) detected at line 1638 [][][] Underfull \hbox (badness 10000) detected at line 1641 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1650--1650 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [316] Underfull \hbox (badness 10000) detected at line 1728 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1736 [][][] [317] Underfull \hbox (badness 10000) detected at line 1766 [][][] Underfull \hbox (badness 10000) detected at line 1769 [][][] Underfull \hbox (badness 10000) detected at line 1803 [][][] Underfull \hbox (badness 10000) detected at line 1806 [][][] [318] Underfull \hbox (badness 10000) detected at line 1840 [][][] Underfull \hbox (badness 10000) detected at line 1843 [][][] [319] Underfull \hbox (badness 10000) detected at line 1877 [][][] Underfull \hbox (badness 10000) detected at line 1880 [][][] Underfull \hbox (badness 10000) detected at line 1883 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 1930 [][][] Underfull \hbox (badness 10000) detected at line 1933 [][][] Underfull \hbox (badness 10000) detected at line 1936 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1945--1945 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [321] Underfull \hbox (badness 10000) detected at line 2031 [][][] Underfull \hbox (badness 10000) detected at line 2034 [][][] [322] Underfull \hbox (badness 10000) detected at line 2068 [][][] Underfull \hbox (badness 10000) detected at line 2071 [][][] Underfull \hbox (badness 10000) detected at line 2074 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2084--2084 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [323] Underfull \hbox (badness 10000) detected at line 2121 [][][] Underfull \hbox (badness 10000) detected at line 2124 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2133--2133 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2168 [][][] Underfull \hbox (badness 10000) detected at line 2171 [][][] [324] Underfull \hbox (badness 10000) detected at line 2203 [][][] Underfull \hbox (badness 10000) detected at line 2206 [][][] [325] Underfull \hbox (badness 10000) detected at line 2242 [][][] Underfull \hbox (badness 10000) detected at line 2245 [][][] Underfull \hbox (badness 10000) detected at line 2281 [][][] Underfull \hbox (badness 10000) detected at line 2284 [][][] [326] Underfull \hbox (badness 10000) detected at line 2312 [][][] Underfull \hbox (badness 10000) detected at line 2315 [][][] Underfull \hbox (badness 10000) detected at line 2318 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2328--2328 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 2365 [][][] Underfull \hbox (badness 10000) detected at line 2368 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 2412 [][][] Underfull \hbox (badness 10000) detected at line 2415 [][][] [329] [330] Underfull \hbox (badness 10000) detected at line 2501 [][][] Underfull \hbox (badness 10000) detected at line 2504 [][][] Underfull \hbox (badness 10000) detected at line 2507 [][][] Underfull \hbox (badness 10000) detected at line 2555 [][][] Underfull \hbox (badness 10000) detected at line 2558 [][][] [331] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2602 [][][] Underfull \hbox (badness 10000) detected at line 2605 [][][] [332] [333] Underfull \hbox (badness 10000) detected at line 2695 [][][] Underfull \hbox (badness 10000) detected at line 2698 [][][] Underfull \hbox (badness 10000) detected at line 2744 [][][] [334] Underfull \hbox (badness 10000) detected at line 2747 [][][] Underfull \hbox (badness 10000) detected at line 2750 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 2797 [][][] Underfull \hbox (badness 10000) detected at line 2800 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2809--2809 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 2844 [][][] Underfull \hbox (badness 10000) detected at line 2847 [][][] Overfull \vbox (9.12637pt too high) has occurred while \output is active [336] Underfull \hbox (badness 10000) detected at line 2903 [][][] Underfull \hbox (badness 10000) detected at line 2906 [][][] [337] Underfull \hbox (badness 10000) detected at line 2944 [][][] Underfull \hbox (badness 10000) detected at line 2955 [][][] Underfull \hbox (badness 10000) detected at line 2958 [][][] [338] Underfull \hbox (badness 10000) detected at line 3044 [][][] Underfull \hbox (badness 10000) detected at line 3047 [][][] [339] Underfull \hbox (badness 10000) detected at line 3050 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3060--3060 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3097 [][][] Underfull \hbox (badness 10000) detected at line 3100 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3109--3109 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [340] Underfull \hbox (badness 10000) detected at line 3144 [][][] Underfull \hbox (badness 10000) detected at line 3147 [][][] [341] Underfull \hbox (badness 10000) detected at line 3185 [][][] Underfull \hbox (badness 10000) detected at line 3188 [][][] Underfull \hbox (badness 10000) detected at line 3191 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3201--3201 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [342] Underfull \hbox (badness 10000) detected at line 3238 [][][] Underfull \hbox (badness 10000) detected at line 3241 [][][] Underfull \hbox (badness 10000) detected at line 3244 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3253--3253 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3286 [][][] [343] [344] Underfull \hbox (badness 10000) detected at line 3340 [][][] [345] [346] Underfull \hbox (badness 10000) detected at line 3482 [][][] Overfull \vbox (42.73187pt too high) has occurred while \output is active [347] Underfull \hbox (badness 10000) detected at line 3540 [][][] Underfull \hbox (badness 10000) detected at line 3543 [][][] [348] Underfull \hbox (badness 10000) detected at line 3583 [][][] Underfull \hbox (badness 10000) detected at line 3586 [][][] Underfull \hbox (badness 10000) detected at line 3589 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3599--3599 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [349] Underfull \hbox (badness 10000) detected at line 3636 [][][] Underfull \hbox (badness 10000) detected at line 3639 [][][] Underfull \hbox (badness 10000) detected at line 3642 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3651--3651 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [350] Underfull \hbox (badness 10000) detected at line 3700 [][][] Underfull \hbox (badness 10000) detected at line 3703 [][][] [351] Underfull \hbox (badness 10000) detected at line 3787 [][][] [352] Underfull \hbox (badness 10000) detected at line 3790 [][][] [353] Underfull \hbox (badness 10000) detected at line 3888 [][][] Underfull \hbox (badness 10000) detected at line 3891 [][][] Underfull \hbox (badness 10000) detected at line 3894 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3904--3904 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [354] Underfull \hbox (badness 10000) detected at line 3941 [][][] Underfull \hbox (badness 10000) detected at line 3944 [][][] Underfull \hbox (badness 10000) detected at line 3970 [][][] Underfull \hbox (badness 10000) detected at line 3973 [][][] [355] Underfull \hbox (badness 10000) detected at line 3999 [][][] Underfull \hbox (badness 10000) detected at line 4002 [][][] [356] Underfull \hbox (badness 10000) detected at line 4032 [][][] Underfull \hbox (badness 10000) detected at line 4035 [][][] Underfull \hbox (badness 10000) detected at line 4038 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4048--4048 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4085 [][][] Underfull \hbox (badness 10000) detected at line 4088 [][][] Underfull \hbox (badness 10000) detected at line 4091 [][][] [357] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4135 [][][] Underfull \hbox (badness 10000) detected at line 4138 [][][] [358] Underfull \hbox (badness 10000) detected at line 4192 [][][] [359] Underfull \hbox (badness 10000) detected at line 4214 [][][] Overfull \vbox (6.64133pt too high) has occurred while \output is active [360] Underfull \hbox (badness 10000) detected at line 4288 [][][] Underfull \hbox (badness 10000) detected at line 4291 [][][] [361] [362] Underfull \hbox (badness 10000) detected at line 4381 [][][] Underfull \hbox (badness 10000) detected at line 4384 [][][] Underfull \hbox (badness 10000) detected at line 4424 [][][] Underfull \hbox (badness 10000) detected at line 4427 [][][] [363] Underfull \hbox (badness 10000) detected at line 4469 [][][] Underfull \hbox (badness 10000) detected at line 4472 [][][] [364] Underfull \hbox (badness 10000) detected at line 4530 [][][] Underfull \hbox (badness 10000) detected at line 4533 [][][] [365] Underfull \hbox (badness 10000) detected at line 4536 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4546--4546 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4583 [][][] Underfull \hbox (badness 10000) detected at line 4586 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4595--4595 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4628 [][][] Underfull \hbox (badness 10000) detected at line 4631 [][][] Underfull \hbox (badness 10000) detected at line 4634 [][][] [367] Underfull \hbox (badness 10000) detected at line 4690 [][][] Underfull \hbox (badness 10000) detected at line 4693 [][][] [368] Underfull \hbox (badness 10000) detected at line 4725 [][][] Underfull \hbox (badness 10000) detected at line 4728 [][][] Underfull \hbox (badness 10000) detected at line 4766 [][][] [369] Underfull \hbox (badness 10000) detected at line 4769 [][][] Underfull \hbox (badness 10000) detected at line 4772 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4782--4782 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] Underfull \hbox (badness 10000) detected at line 4820 [][][] Underfull \hbox (badness 10000) detected at line 4823 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4832--4832 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [370] Underfull \hbox (badness 10000) detected at line 4867 [][][] Underfull \hbox (badness 10000) detected at line 4870 [][][] [371] Underfull \hbox (badness 10000) detected at line 4928 [][][] Underfull \hbox (badness 10000) detected at line 4931 [][][] Underfull \hbox (badness 10000) detected at line 4963 [][][] [372] Underfull \hbox (badness 10000) detected at line 4966 [][][] Underfull \hbox (badness 10000) detected at line 4969 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4979--4979 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 5016 [][][] Underfull \hbox (badness 10000) detected at line 5019 [][][] Underfull \hbox (badness 10000) detected at line 5022 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5031--5031 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [373] Underfull \hbox (badness 10000) detected at line 5066 [][][] Underfull \hbox (badness 10000) detected at line 5069 [][][] [374] Underfull \hbox (badness 10000) detected at line 5099 [][][] Underfull \hbox (badness 10000) detected at line 5102 [][][] Underfull \hbox (badness 10000) detected at line 5105 [][][] Underfull \hbox (badness 10000) detected at line 5135 [][][] Underfull \hbox (badness 10000) detected at line 5138 [][][] [375] Underfull \hbox (badness 10000) detected at line 5168 [][][] Underfull \hbox (badness 10000) detected at line 5171 [][][] Underfull \hbox (badness 10000) detected at line 5201 [][][] [376] Underfull \hbox (badness 10000) detected at line 5204 [][][] Underfull \hbox (badness 10000) detected at line 5232 [][][] Underfull \hbox (badness 10000) detected at line 5235 [][][] [377] Underfull \hbox (badness 10000) detected at line 5263 [][][] Underfull \hbox (badness 10000) detected at line 5266 [][][] ) (./group___frontend.tex Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [378] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [379] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [380] [381] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [382] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] [383] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [384] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [385] [386] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [387] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [388] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [389] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] [390] Underfull \hbox (badness 10000) detected at line 748 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] [391] Underfull \hbox (badness 10000) detected at line 818 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] [392] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] [393] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] [394] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] [395] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Overfull \vbox (27.00906pt too high) has occurred while \output is active [396] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] [397] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] [398] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] [399] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Underfull \hbox (badness 10000) detected at line 1348 [][][] [400] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] [401] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] [402] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] Underfull \hbox (badness 10000) detected at line 1562 [][][] [403] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [404] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Underfull \hbox (badness 10000) detected at line 1688 [][][] [405] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Underfull \hbox (badness 10000) detected at line 1747 [][][] [406] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] Underfull \hbox (badness 10000) detected at line 1809 [][][] [407] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [408] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [409]) (./structs_a_p_o_lparm.tex [410] Underfull \hbox (badness 10000) detected at line 88 [][][] [411] [412] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [413] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [414] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [415]) (./structs_b_e_mparm.tex [416] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [417] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [418] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [419] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [420] [421] [422]) (./structs_g_e_o_f_l_o_wparm.tex [423] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [424]) (./structs_m_gparm.tex [425] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) in paragraph at lines 149--150 [426] Underfull \hbox (badness 10000) in paragraph at lines 180--181 [427] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [428] [429] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] [430] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [431] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [432] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [433] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [434] Underfull \hbox (badness 10000) detected at line 108 [][][] [435] [436] [437] [438] [439] [440]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) detected at line 38 [][][] [441] [442]) (./structs_p_b_a_mparm.tex [443] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [444] [445] [446] [447] [448]) (./structs_p_b_eparm.tex [449] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [450] [451] [452] Underfull \hbox (badness 10000) detected at line 391 [][][] [453] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [454] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [455] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [456] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [457] [458]) (./structs_p_b_s_a_mparm.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [460] [461]) (./structs_vacc.tex [462] Underfull \hbox (badness 10000) detected at line 36 [][][] [463]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [464]) (./structs_valist.tex [465] Underfull \hbox (badness 10000) detected at line 36 [][][] [466]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [467] Underfull \hbox (badness 10000) in paragraph at lines 62--63 Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 [468]) (./structs_vclist.tex Underfull \hbox (badness 10000) detected at line 40 [][][] [469]) (./structs_vclist_cell.tex [470] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [471] Underfull \hbox (badness 10000) detected at line 42 [][][] [472]) (./structs_vfetk.tex [473] Underfull \hbox (badness 10000) detected at line 60 [][][] [474] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [475] [476]) (./structs_vfetk___local_var.tex [477] Underfull \hbox (badness 10000) detected at line 86 [][][] [478] [479] [480] [481]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [482]) (./structs_vgrid.tex [483] Underfull \hbox (badness 10000) detected at line 52 [][][] [484] [485]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] [486]) (./structs_vopot.tex Underfull \hbox (badness 10000) detected at line 26 [][][] [487]) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [488]) (./structs_vpbe.tex [489] Underfull \hbox (badness 10000) detected at line 86 [][][] [490] [491] [492] [493]) (./structs_vpee.tex [494] Underfull \hbox (badness 10000) detected at line 34 [][][] [495]) (./structs_vpmg.tex [496] Underfull \hbox (badness 10000) detected at line 116 [][][] [497] [498] [499] [500] [501] [502]) (./structs_vpmgp.tex [503] Underfull \hbox (badness 10000) detected at line 126 [][][] [504] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [505] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [506] [507] [508] [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 Underfull \hbox (badness 10000) in paragraph at lines 548--549 [511] Underfull \hbox (badness 10000) in paragraph at lines 589--590 Underfull \hbox (badness 10000) in paragraph at lines 630--631 [512] Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [513] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) detected at line 28 [][][] [514]) [515] [516] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex) (./apbs_8h_source.tex [517]) (./vcsm_8c.tex [518] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [519]) (./vcsm_8c_source.tex [520] [521] [522] [523] [524] [525]) (./vcsm_8h.tex [526] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [527]) (./vcsm_8h_source.tex [528]) (./vfetk_8c.tex [529] [530] [531] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] [532] [533] [534] [535] [536] [537]) (./vfetk_8c_source.tex [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567]) (./vfetk_8h.tex [568] [569] [570] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [571]) (./vfetk_8h_source.tex [572] [573] [574] [575] [576]) (./vpee_8c.tex [577] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [578]) (./vpee_8c_source.tex [579] [580] [581] [582] [583] [584] [585]) (./vpee_8h.tex Underfull \hbox (badness 10000) detected at line 45 [][][] [586] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vpee_8h_source.tex [587]) (./apolparm_8c.tex [588] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [589] [590] [591]) (./apolparm_8c_source.tex [592] [593] [594] [595] [596] [597] [598]) (./apolparm_8h_source.tex [599]) (./bemparm_8c.tex [600] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [601] Underfull \hbox (badness 10000) detected at line 115 [][][] [602]) (./bemparm_8c_source.tex [603] [604] [605] [606]) (./bemparm_8h_source.tex [607]) (./femparm_8c.tex Underfull \hbox (badness 10000) detected at line 53 [][][] [608] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [609] [610]) (./femparm_8c_source.tex [611] [612] [613] [614] [615]) (./femparm_8h.tex [616] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [617]) (./femparm_8h_source.tex [618]) (./geoflowparm_8c.tex [619] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [620]) (./geoflowparm_8c_source.tex [621] [622] [623]) (./geoflowparm_8h.tex [624] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [625]) (./geoflowparm_8h_source.tex [626]) (./mgparm_8c.tex [627] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [628] [629] [630]) (./mgparm_8c_source.tex [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642]) (./mgparm_8h.tex [643] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [644]) (./mgparm_8h_source.tex [645] [646]) (./nosh_8c.tex [647] [648] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [649] [650] [651] [652] [653] [654]) (./nosh_8c_source.tex [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694]) (./nosh_8h.tex [695] [696] [697] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./nosh_8h_source.tex [698] [699] [700]) (./pbamparm_8c.tex [701] [702] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] [703]) (./pbamparm_8c_source.tex [704] [705] [706] [707] [708] [709] [710] [711]) (./pbamparm_8h.tex [712] [713] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] [714]) (./pbamparm_8h_source.tex [715] [716]) (./pbeparm_8c.tex [717] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [718] [719] [720] [721] [722]) (./pbeparm_8c_source.tex [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737]) (./pbeparm_8h.tex [738] Underfull \hbox (badness 10000) detected at line 76 [][][] [739] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] ) (./pbeparm_8h_source.tex [740] [741]) (./pbsamparm_8c.tex [742] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [743]) (./pbsamparm_8c_source.tex [744] [745] [746]) (./pbsamparm_8h.tex [747] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [748] Underfull \hbox (badness 10000) detected at line 80 [][][] [749]) (./pbsamparm_8h_source.tex [750]) (./vacc_8c.tex [751] [752] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [753] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Overfull \vbox (5.66235pt too high) has occurred while \output is active [754] [755]) (./vacc_8c_source.tex [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778]) (./vacc_8h.tex [779] [780] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [781]) (./vacc_8h_source.tex [782] [783] [784] [785]) (./valist_8c.tex Underfull \hbox (badness 2293) in paragraph at lines 48--50 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] [786] Underfull \hbox (badness 10000) detected at line 76 [][][] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] [787] [788] [789]) (./valist_8c_source.tex [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800]) (./valist_8h.tex [801] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [802]) (./valist_8h_source.tex [803]) (./vatom_8c.tex [804] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [805] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex [809] [810] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [811]) (./vatom_8h_source.tex [812]) (./vcap_8c.tex [813] Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 31 [][][] [814]) (./vcap_8c_source.tex) (./vcap_8h.tex [815] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [816]) (./vcap_8h_source.tex) (./vclist_8c.tex [817] Underfull \hbox (badness 4060) in paragraph at lines 26--28 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] Underfull \hbox (badness 1297) in paragraph at lines 38--39 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m /n/10 thee, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 alist, dou-ble max[]_[]radi us, int npts[][][], Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [818] [819]) (./vclist_8c_source.tex [820] [821] [822] [823] [824] [825]) (./vclist_8h.tex [826] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [827]) (./vclist_8h_source.tex [828] [829]) (./vgreen_8c.tex [830] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [831]) (./vgreen_8c_source.tex [832] [833] [834] [835] [836] [837]) (./vgreen_8h.tex [838] [839] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] ) (./vgreen_8h_source.tex [840]) (./vhal_8h.tex [841] [842] [843] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 294 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [844] [845] [846] [847] [848] [849] [850] [851]) (./vhal_8h_source.tex [852] [853] [854] [855] [856] [857] [858] [859]) (./vmatrix_8h.tex [860] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [861] [862]) (./vmatrix_8h_source.tex) (./vparam_8c.tex [863] [864] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] [865]) (./vparam_8c_source.tex [866] [867] [868] [869] [870] [871] [872] [873]) (./vparam_8h.tex [874] [875] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] ) (./vparam_8h_source.tex [876] [877]) (./vpbe_8c.tex [878] Underfull \hbox (badness 10000) detected at line 84 [][][] [879] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [880]) (./vpbe_8c_source.tex [881] [882] [883] [884] [885] [886]) (./vpbe_8h.tex [887] [888] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./vpbe_8h_source.tex [889] [890] [891]) (./vstring_8c.tex Underfull \hbox (badness 10000) detected at line 25 [][][] Underfull \hbox (badness 10000) detected at line 28 [][][] [892] Underfull \hbox (badness 10000) detected at line 31 [][][] ) (./vstring_8c_source.tex [893] [894]) (./vstring_8h.tex [895] Underfull \hbox (badness 10000) detected at line 29 [][][] Underfull \hbox (badness 10000) detected at line 32 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] [896]) (./vstring_8h_source.tex) (./vunit_8h.tex [897] LaTeX Warning: Command \r invalid in math mode on input line 36. Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [898]) (./vunit_8h_source.tex) (./main_8c.tex [899] Underfull \hbox (badness 10000) detected at line 22 [][][] Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [900]) (./main_8c_source.tex [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911]) (./vgrid_8c.tex [912] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [913] [914] Underfull \hbox (badness 10000) detected at line 163 [][][] [915]) (./vgrid_8c_source.tex [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938]) (./vgrid_8h.tex [939] [940] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [941] Underfull \hbox (badness 10000) detected at line 153 [][][] ) (./vgrid_8h_source.tex [942] [943]) (./vmgrid_8c.tex Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] [944] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 53--53 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [945] [946]) (./vmgrid_8h.tex [947] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [948]) (./vmgrid_8h_source.tex [949]) (./vopot_8c.tex [950] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [951]) (./vopot_8c_source.tex [952] [953] [954] [955]) (./vopot_8h.tex [956] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] ) (./vopot_8h_source.tex [957]) (./vpmg_8c.tex [958] [959] [960] [961] Underfull \hbox (badness 10000) detected at line 167 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] [962] Underfull \hbox (badness 10000) detected at line 255 [][][] [963] Underfull \hbox (badness 10000) detected at line 282 [][][] [964] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [965] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 456 [][][] [966] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] [967] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [968] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 653 [][][] Underfull \hbox (badness 10000) detected at line 670 [][][] [969] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 711 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 745 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] [970] Underfull \hbox (badness 10000) detected at line 789 [][][] [971] Underfull \hbox (badness 10000) detected at line 826 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] [972] Underfull \hbox (badness 10000) detected at line 920 [][][] [973] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 964 [][][] [974] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 989 [][][] Underfull \hbox (badness 10000) detected at line 1006 [][][] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] [975] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [976] Underfull \hbox (badness 10000) detected at line 1108 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] ) (./vpmg_8c_source.tex [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]) (./vpmg_8h.tex [1113] [1114] [1115] [1116] [1117] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [1118] [1119] [1120] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [1121] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [1122] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 510 [][][] Underfull \hbox (badness 10000) detected at line 532 [][][] Underfull \hbox (badness 10000) detected at line 535 [][][] [1123] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 560 [][][] Underfull \hbox (badness 10000) detected at line 582 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [1124] Underfull \hbox (badness 10000) detected at line 627 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] [1125] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 773 [][][] [1126] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] [1127] Underfull \hbox (badness 10000) detected at line 871 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 901 [][][] [1128] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] [1129] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [1130] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1089 [][][] [1131] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [1132] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] ) (./vpmg_8h_source.tex [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]) (./vpmgp_8c.tex Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [1142] Underfull \hbox (badness 10000) detected at line 39 [][][] ) (./vpmgp_8c_source.tex [1143] [1144] [1145] [1146]) (./vpmgp_8h.tex [1147] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [1148]) (./vpmgp_8h_source.tex [1149]) (./build_ad_8c_source.tex [1150] [1151] [1152]) (./build_ad_8h_source.tex [1153] [1154]) (./build_bd_8c_source.tex [1155] [1156] [1157]) (./build_bd_8h_source.tex [1158]) (./build_gd_8c_source.tex [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196]) (./build_gd_8h_source.tex [1197] [1198]) (./build_pd_8c_source.tex [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217]) (./build_pd_8h_source.tex [1218] [1219] [1220]) (./cgd_8c_source.tex [1221]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1222] [1223] [1224] [1225]) (./gsd_8h_source.tex [1226]) (./matvecd_8c_source.tex [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./matvecd_8h_source.tex [1240] [1241] [1242] [1243] [1244] [1245]) (./mgcsd_8c_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8h_source.tex [1252]) (./mgdrvd_8c_source.tex [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260]) (./mgdrvd_8h_source.tex [1261]) (./mgfasd_8c_source.tex [1262] [1263] [1264] [1265] [1266] [1267] [1268]) (./mgfasd_8h_source.tex [1269]) (./mgsubd_8c_source.tex [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280]) (./mgsubd_8h_source.tex [1281] [1282] [1283] [1284]) (./mikpckd_8c_source.tex [1285] [1286] [1287] [1288] [1289]) (./mikpckd_8h_source.tex [1290] [1291]) (./mlinpckd_8c_source.tex [1292] [1293]) (./mlinpckd_8h_source.tex [1294]) (./mypdec_8c_source.tex [1295] [1296] [1297] [1298] [1299] [1300]) (./mypdec_8h_source.tex [1301]) (./newdrvd_8c_source.tex [1302] [1303] [1304] [1305]) (./newdrvd_8h_source.tex [1306]) (./newtond_8c_source.tex [1307] [1308] [1309] [1310] [1311] [1312] [1313]) (./newtond_8h_source.tex [1314]) (./powerd_8c_source.tex [1315] [1316] [1317] [1318] [1319]) (./powerd_8h_source.tex [1320]) (./smoothd_8c_source.tex [1321]) (./smoothd_8h_source.tex [1322]) (./routines_8c.tex [1323] Underfull \hbox (badness 776) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 42--43 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 42--43 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 56--57 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 62--63 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 64--65 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1324] Underfull \hbox (badness 1442) in paragraph at lines 76--77 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 84--85 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1325] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./routines_8c_source.tex [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394]) (./routines_8h.tex Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], [1395] Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1396] Underfull \hbox (badness 2495) in paragraph at lines 112--113 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1397] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] [1398]) (./routines_8h_source.tex [1399] [1400] [1401] [1402]) [1403] [1404] (./refman.ind [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb> Output written on refman.pdf (1511 pages, 5646846 bytes). Transcript written on refman.log. make[3]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/latex' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 55%] Built target doc-pdf make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mgmesh make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 57%] Built target mgmesh make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target smooth make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 59%] Built target smooth make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dxmath make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 62%] Built target dxmath make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mergedx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 64%] Built target mergedx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mergedx2 make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 66%] Built target mergedx2 make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target value make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 68%] Built target value make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target multivalue make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 71%] Built target multivalue make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target benchmark make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 73%] Built target benchmark make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target similarity make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 75%] Built target similarity make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target analysis make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 78%] Built target analysis make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dx2mol make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 80%] Built target dx2mol make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dx2uhbd make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 82%] Built target dx2uhbd make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target del2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 85%] Built target del2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target tensor2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 87%] Built target tensor2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target uhbd_asc2bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 89%] Built target uhbd_asc2bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target coulomb make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 91%] Built target coulomb make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target born make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 94%] Built target born make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Built target apbslib_swig_compilation make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target _apbslib make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 97%] Built target _apbslib make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target iapbs make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [100%] Built target iapbs make[1]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' Install the project... -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs/doc/programmer -- 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-- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs/tools/bin/tensor2dx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs/tools/bin/coulomb -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs/tools/bin/born -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/libapbs.so.1 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/libapbs.so.1" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/libapbs.so -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/apbscfg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/apbs.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/routines.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/nosh.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/mgparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/femparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/pbamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/pbsamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/pbeparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/bemparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/geoflowparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/apolparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vacc.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/valist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vatom.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vpbe.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vcap.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vclist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vstring.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vparam.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vgreen.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vmatrix.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vhal.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/generic/vunit.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/buildAd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/buildBd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/buildGd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/buildPd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/cgd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/gsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/matvecd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mgcsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mgsubd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mikpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mypdec.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/newtond.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/newdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/powerd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/smoothd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/pmgc/mgfasd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/mg/vgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/mg/vmgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/mg/vopot.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/mg/vpmg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/apbs/mg/vpmgp.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mgmesh -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mgmesh" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/smooth -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/smooth" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dxmath -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dxmath" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx2 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx2" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/value -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/value" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/multivalue -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/multivalue" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/benchmark -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/benchmark" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/similarity -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/similarity" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/analysis -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/analysis" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2mol -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2mol" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2uhbd -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2uhbd" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/del2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/del2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/tensor2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/tensor2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/uhbd_asc2bin -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/uhbd_asc2bin" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/coulomb -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/coulomb" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/born -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/born" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib/libiapbs.a -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/include/iapbs/apbs_driver.h make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/coulomb + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/coulomb /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-coulomb + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/coulomb + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/born + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/born /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-born + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/born + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mgmesh + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mgmesh /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mgmesh + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mgmesh + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dxmath + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dxmath /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dxmath + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dxmath + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx2 + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx2 /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx2 + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx2 + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/mergedx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/value + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/value /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-value + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/value + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/uhbd_asc2bin + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/uhbd_asc2bin /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-uhbd_asc2bin + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/uhbd_asc2bin + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/smooth + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/smooth /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-smooth + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/smooth + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2mol + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2mol /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2mol + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2mol + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2uhbd + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2uhbd /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2uhbd + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/dx2uhbd + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/similarity + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/similarity /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-similarity + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/similarity + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/multivalue + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/multivalue /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-multivalue + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/multivalue + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/benchmark + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/benchmark /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-benchmark + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/benchmark + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/analysis + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/analysis /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-analysis + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/analysis + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/del2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/del2dx /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-del2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/del2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/tensor2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/tensor2dx /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-tensor2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/tensor2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-coulomb + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-born + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mgmesh + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dxmath + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx2 + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-value + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-uhbd_asc2bin + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-smooth + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2mol + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2uhbd + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-similarity + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-multivalue + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-benchmark + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-analysis + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-del2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-tensor2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/libapbs.so.1 + mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs + install -pm 755 tools/manip/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs/ + pathfix.py -pn -i /usr/bin/python3 /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs/psize.py: updating + ln -s /usr/lib64/python3.11/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-psize.py + install -pm 755 build/lib/_apbslib.so /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs/ + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/apbs ++ find /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 -type f '(' -name '*.a' ')' + for i in `find /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 -type f \( -name "*.a" \)` + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib/libiapbs.a + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 3.0.0-16.fc37 --unique-debug-suffix -3.0.0-16.fc37.aarch64 --unique-debug-src-base apbs-3.0.0-16.fc37.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/apbs-3.0.0 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-benchmark extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-coulomb extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-born extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-analysis extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-del2dx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2mol extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dx2uhbd extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-dxmath extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mergedx2 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-mgmesh extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-multivalue extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-similarity extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-smooth extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-tensor2dx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-uhbd_asc2bin extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/bin/apbs-value extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/libapbs.so.1 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11/site-packages/apbs/_apbslib.so original debug info size: 4500kB, size after compression: 4028kB /usr/bin/sepdebugcrcfix: Updated 20 CRC32s, 0 CRC32s did match. 5153 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib/debug/usr/lib64/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.I6XiM1 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/apbs-3.0.0/.package_note-apbs-3.0.0-16.fc37.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh apbs 3.0.0-16.fc37 aarch64 + cd apbs-3.0.0 + pushd tests ~/build/BUILD/apbs-3.0.0/tests ~/build/BUILD/apbs-3.0.0 + export LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/lib64 + /usr/bin/python3 ./apbs_tester.py Testing all sections The following sections will be tested: born, actin-dimer-auto, actin-dimer-parallel, alkanes, FKBP, hca-bind, ionize, ion-pmf, ion-protein, pka-lig, point-pmf, solv ================================================================================ Running tests for born section -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001998 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 960.7073836227 RESULT 2200.266567971 RESULT 4732.245131587 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.7735526282 Testing computed result 9.607073836227E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 2.200266567971E+03 against expected result 2.200267E+03 *** PASSED *** Testing computed result 4.732245131587E+03 against expected result 4.732245E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 *** PASSED *** Elapsed time: 2.989328 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 953.292876745 RESULT 2201.243880085 RESULT 4733.006258977 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.0124252387 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 2.201243880085E+03 against expected result 2.201244E+03 *** PASSED *** Testing computed result 4.733006258977E+03 against expected result 4.733006E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 *** PASSED *** Elapsed time: 2.872378 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 2.401768459022E+02 8.142935592471E+02 1.485255308186E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.761864094552E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 2.401768459022E+02 8.142778312125E+02 1.485246667424E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.762728170718E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605695E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 2.401768459091E+02 8.142935605695E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 2.401768459091E+02 8.142778325440E+02 1.485246665692E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.762728344953E+01 RESULT 960.7073836226 RESULT 3257.1427835730997 RESULT 5941.0039478710005 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -230.49184867462003 Testing computed result 9.607073836226E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 3.257142783573E+03 against expected result 3.257143E+03 *** PASSED *** Testing computed result 5.941003947871E+03 against expected result 5.941004E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 *** PASSED *** Elapsed time: 14.427871 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 2.383232191816E+02 8.145369591602E+02 1.485524998001E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734895113069E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 2.383232191816E+02 8.145419898332E+02 1.485529328612E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734462051928E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 2.383232191909E+02 8.145369593489E+02 1.485524997676E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734895146550E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 2.383232191909E+02 8.145419900310E+02 1.485529328301E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734462084052E+01 RESULT 953.292876745 RESULT 3258.1578983732998 RESULT 5942.108652589999 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -229.38714395599 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 3.258157898373E+03 against expected result 3.258158E+03 *** PASSED *** Testing computed result 5.942108652590E+03 against expected result 5.942109E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 *** PASSED *** Elapsed time: 13.345285 seconds -------------------------------------------------------------------------------- Total elapsed time: 33.636860 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 152761.7850342 RESULT 291951.0754196 RESULT 152767.184488 RESULT 291546.8859278 RESULT 305631.7807611 RESULT 583602.8296532 RESULT 104.8683058621 Testing computed result 1.527617850342E+05 against expected result 1.527618E+05 *** PASSED *** Testing computed result 2.919510754196E+05 against expected result 2.919511E+05 *** PASSED *** Testing computed result 1.527671844880E+05 against expected result 1.527672E+05 *** PASSED *** Testing computed result 2.915468859278E+05 against expected result 2.915469E+05 *** PASSED *** Testing computed result 3.056317807611E+05 against expected result 3.056318E+05 *** PASSED *** Testing computed result 5.836028296532E+05 against expected result 5.836028E+05 *** PASSED *** Testing computed result 1.048683058621E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 185.759162 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 152863.2421825 RESULT 292061.866232 RESULT 152929.7900572 RESULT 291659.2202835 RESULT 305924.4262535 RESULT 583830.6706232 RESULT 109.5841077688 Testing computed result 1.528632421825E+05 against expected result 1.528632E+05 *** PASSED *** Testing computed result 2.920618662320E+05 against expected result 2.920619E+05 *** PASSED *** Testing computed result 1.529297900572E+05 against expected result 1.529298E+05 *** PASSED *** Testing computed result 2.916592202835E+05 against expected result 2.916592E+05 *** PASSED *** Testing computed result 3.059244262535E+05 against expected result 3.059244E+05 *** PASSED *** Testing computed result 5.838306706232E+05 against expected result 5.838307E+05 *** PASSED *** Testing computed result 1.095841077688E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 150.190633 seconds -------------------------------------------------------------------------------- Total elapsed time: 335.949795 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-parallel section -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.335181353180E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.307364296734E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.892640552270E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.287358143371E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.237489755360E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595556932858E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.344927525614E+00 kJ/mol Global net ELEC energy = 8.344927525614E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 1.335181353180E+03 1.307364296734E+04 2.892640552270E+03 2.287358143371E+04 4.237489755360E+03 3.595556932858E+04 8.344927525614E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161150884899E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.271350510933E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.084559511557E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.159029781186E-02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161009682231E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.271251267660E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -9.008424333884E-01 kJ/mol Global net ELEC energy = -9.008424333884E-01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 1.161150884899E+04 9.271350510933E+04 1.084559511557E-01 9.159029781186E-02 1.161009682231E+04 9.271251267660E+04 -9.008424333884E-01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.533327920982E+01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.349327483109E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.753646268927E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.716901575464E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.760706267384E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.753396861378E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.002011083294E+01 kJ/mol Global net ELEC energy = 3.002011083294E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 1.533327920982E+01 3.349327483109E+02 4.753646268927E+03 3.716901575464E+04 4.760706267384E+03 3.753396861378E+04 3.002011083294E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.803290534287E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.400275505449E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.150603559111E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.573366340513E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.804039178218E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.400354034488E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.710240552064E+00 kJ/mol Global net ELEC energy = 8.710240552064E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 1.803290534287E+04 1.400275505449E+05 8.150603559111E-01 8.573366340513E-01 1.804039178218E+04 1.400354034488E+05 8.710240552064E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.015087619451E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.216054444942E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.620207421716E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.273875108812E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.666622027749E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306246500367E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.108471049009E+01 kJ/mol Global net ELEC energy = 2.108471049009E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE4.out Processor 4 results: 4.015087619451E+02 3.216054444942E+03 1.620207421716E+04 1.273875108812E+05 1.666622027749E+04 1.306246500367E+05 2.108471049009E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.100112513614E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.662571945373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.370921758038E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.012777153962E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.115105077953E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.662769018146E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.372005444809E+00 kJ/mol Global net ELEC energy = 2.372005444809E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE5.out Processor 5 results: 2.100112513614E+03 1.662571945373E+04 4.370921758038E-01 4.012777153962E-01 2.115105077953E+03 1.662769018146E+04 2.372005444809E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.817378781616E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.959534462269E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176793266728E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.643533578081E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176229449467E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.643148330287E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.892943480303E+00 kJ/mol Global net ELEC energy = -1.892943480303E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE6.out Processor 6 results: 2.817378781616E+00 1.959534462269E+00 1.176793266728E+04 9.643533578081E+04 1.176229449467E+04 9.643148330287E+04 -1.892943480303E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.428230292158E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.199832997920E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.881300088062E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.152799174875E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.847712854852E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618156668929E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.043753521021E+01 kJ/mol Global net ELEC energy = 3.043753521021E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE7.out Processor 7 results: 2.428230292158E+03 2.199832997920E+04 3.881300088062E+02 4.152799174875E+03 2.847712854852E+03 2.618156668929E+04 3.043753521021E+01 RESULT 35927.59777074854 RESULT 287991.6947822151 RESULT 36005.78432292607 RESULT 288019.59322988224 RESULT 72040.017332199 RESULT 576102.84427808 RESULT 98.1757441420356 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916947822E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195932299E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028442781E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817574414204E+01 against expected result 9.817456E+01 *** PASSED (with rounding error - see log) *** Elapsed time: 561.339655 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.371266245949E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.306912290219E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977036667733E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.288057507497E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.356039288708E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595843060209E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.732624922090E+00 kJ/mol Global net ELEC energy = 8.732624922090E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 1.371266245949E+03 1.306912290219E+04 2.977036667733E+03 2.288057507497E+04 4.356039288708E+03 3.595843060209E+04 8.732624922090E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183935033618E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.276169789420E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.420924995464E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.129030298944E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183791435221E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.276043001853E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.154972633314E+00 kJ/mol Global net ELEC energy = -1.154972633314E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 1.183935033618E+04 9.276169789420E+04 1.420924995464E-01 1.129030298944E-01 1.183791435221E+04 9.276043001853E+04 -1.154972633314E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.992726432058E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.375960934473E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.863608503641E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.720602537782E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.896854387650E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.757590620855E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.228473728522E+01 kJ/mol Global net ELEC energy = 3.228473728522E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 9.992726432058E+00 3.375960934473E+02 4.863608503641E+03 3.720602537782E+04 4.896854387650E+03 3.757590620855E+04 3.228473728522E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.826846317904E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.401007397614E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.966525690477E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.961424692860E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827933209233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.401092487740E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 9.405155088186E+00 kJ/mol Global net ELEC energy = 9.405155088186E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 1.826846317904E+04 1.401007397614E+05 9.966525690477E-01 8.961424692860E-01 1.827933209233E+04 1.401092487740E+05 9.405155088186E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.021998204986E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.215581391535E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.644646339930E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.274227987774E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.689865332202E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306747563963E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.637622734662E+01 kJ/mol Global net ELEC energy = 3.637622734662E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE4.out Processor 4 results: 4.021998204986E+02 3.215581391535E+03 1.644646339930E+04 1.274227987774E+05 1.689865332202E+04 1.306747563963E+05 3.637622734662E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.187673595319E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.663590090053E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.710032885061E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.848912615891E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189033693728E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.663642086377E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 1.004854500183E+00 kJ/mol Global net ELEC energy = 1.004854500183E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE5.out Processor 5 results: 2.187673595319E+03 1.663590090053E+04 4.710032885061E-01 4.848912615891E-01 2.189033693728E+03 1.663642086377E+04 1.004854500183E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.897659240526E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.552765434658E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.200266111088E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.646358551314E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.199560371894E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.645933328248E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.699465221137E+00 kJ/mol Global net ELEC energy = -1.699465221137E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE6.out Processor 6 results: 4.897659240526E+00 2.552765434658E+00 1.200266111088E+04 9.646358551314E+04 1.199560371894E+04 9.645933328248E+04 -1.699465221137E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.521894873214E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200161660501E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.033680106430E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.154432431334E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.960165191413E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618664307349E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.059403714563E+01 kJ/mol Global net ELEC energy = 3.059403714563E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE7.out Processor 7 results: 2.521894873214E+03 2.200161660501E+04 4.033680106430E+02 4.154432431334E+03 2.960165191413E+03 2.618664307349E+04 3.059403714563E+01 RESULT 36605.73843587318 RESULT 288124.808313747 RESULT 36694.74744055409 RESULT 288128.91111142474 RESULT 73413.59604699901 RESULT 576361.16921921 RESULT 115.54319843347798 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881248083137E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289111114E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611692192E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155431984335E+02 against expected result 1.155421E+02 *** PASSED (with rounding error - see log) *** Elapsed time: 492.020029 seconds -------------------------------------------------------------------------------- Total elapsed time: 1053.359684 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: alkanes.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Checking for intermidiate energies in input file alkanes.out RESULT 14.39739455792 RESULT 12.08346456826 RESULT 13.54016672221 RESULT 9.363673200142 RESULT 9.422717598546 RESULT 16.40068943201 RESULT 13.23144287435 RESULT 7.894367190329 RESULT 14.49633815052 RESULT 14.47900211546 RESULT 11.92358496286 Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 *** PASSED *** Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 *** PASSED *** Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 *** PASSED *** Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 *** PASSED *** Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 *** PASSED *** Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 *** PASSED *** Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 *** PASSED *** Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 *** PASSED *** Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 *** PASSED *** Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 *** PASSED *** Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 *** PASSED *** Elapsed time: 34.144894 seconds -------------------------------------------------------------------------------- Total elapsed time: 34.144894 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-mol.out RESULT 10608.99690259 RESULT 42765.23673491 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 39.61107503213 RESULT 712.1048606059 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10584.10584089 RESULT 42053.85249581 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3335.429017008 RESULT -21.80527370616 RESULT -3328.631844166 RESULT 15.00810086373 Testing computed result 1.060899690259E+04 against expected result 1.060900E+04 *** PASSED *** Testing computed result 4.276523673491E+04 against expected result 4.276524E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.961107503213E+01 against expected result 3.961108E+01 *** PASSED *** Testing computed result 7.121048606059E+02 against expected result 7.121049E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.058410584089E+04 against expected result 1.058411E+04 *** PASSED *** Testing computed result 4.205385249581E+04 against expected result 4.205385E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.500810086373E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 23.148964 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-smol.out RESULT 10749.48704824 RESULT 42894.87256481 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 37.19709905887 RESULT 712.5747080979 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10716.54753674 RESULT 42181.78203716 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3205.793187109 RESULT -21.33542621421 RESULT -3200.702302816 RESULT 16.24454192074 Testing computed result 1.074948704824E+04 against expected result 1.074949E+04 *** PASSED *** Testing computed result 4.289487256481E+04 against expected result 4.289487E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.719709905887E+01 against expected result 3.719710E+01 *** PASSED *** Testing computed result 7.125747080979E+02 against expected result 7.125747E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.071654753674E+04 against expected result 1.071655E+04 *** PASSED *** Testing computed result 4.218178203716E+04 against expected result 4.218178E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.624454192074E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 22.506069 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-mol.out RESULT 9160.578033846 RESULT 39557.01871716 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 94.31133325426 RESULT 1677.348113184 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9040.108332204 RESULT 37877.47796627 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -3460.997931137 RESULT -20.52167100108 RESULT -3454.901259473 RESULT 14.42499933664 Testing computed result 9.160578033846E+03 against expected result 9.160578E+03 *** PASSED *** Testing computed result 3.955701871716E+04 against expected result 3.955702E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 9.431133325426E+01 against expected result 9.431133E+01 *** PASSED *** Testing computed result 1.677348113184E+03 against expected result 1.677348E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.040108332204E+03 against expected result 9.040108E+03 *** PASSED *** Testing computed result 3.787747796627E+04 against expected result 3.787748E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.442499933664E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 23.019967 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-smol.out RESULT 9634.884642408 RESULT 40031.77540425 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 79.42232645345 RESULT 1677.798535473 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9507.068451372 RESULT 38350.75772299 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -2986.24124404 RESULT -20.07124871262 RESULT -2981.621502756 RESULT 15.45150742843 Testing computed result 9.634884642408E+03 against expected result 9.634885E+03 *** PASSED *** Testing computed result 4.003177540425E+04 against expected result 4.003178E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 7.942232645345E+01 against expected result 7.942233E+01 *** PASSED *** Testing computed result 1.677798535473E+03 against expected result 1.677799E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.507068451372E+03 against expected result 9.507068E+03 *** PASSED *** Testing computed result 3.835075772299E+04 against expected result 3.835076E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.545150742843E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 22.189930 seconds -------------------------------------------------------------------------------- Total elapsed time: 90.864930 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 221.3600726771 RESULT 1825.764811255 RESULT 6458.471211905 RESULT 20936.06095527 RESULT 151543.3544464 RESULT 178636.9323561 RESULT 21053.22784838 RESULT 153330.4996252 RESULT 185042.9388099 RESULT -52.46475812684 Testing computed result 2.213600726771E+02 against expected result 2.213601E+02 *** PASSED *** Testing computed result 1.825764811255E+03 against expected result 1.825765E+03 *** PASSED *** Testing computed result 6.458471211905E+03 against expected result 6.458471E+03 *** PASSED *** Testing computed result 2.093606095527E+04 against expected result 2.093606E+04 *** PASSED *** Testing computed result 1.515433544464E+05 against expected result 1.515434E+05 *** PASSED *** Testing computed result 1.786369323561E+05 against expected result 1.786369E+05 *** PASSED *** Testing computed result 2.105322784838E+04 against expected result 2.105323E+04 *** PASSED *** Testing computed result 1.533304996252E+05 against expected result 1.533305E+05 *** PASSED *** Testing computed result 1.850429388099E+05 against expected result 1.850429E+05 *** PASSED *** Testing computed result -5.246475812684E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 22.009408 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 188.4888131017 RESULT 1820.045922544 RESULT 6460.002606908 RESULT 21891.61497021 RESULT 152000.0494925 RESULT 179043.619158 RESULT 21958.42512312 RESULT 153777.1604355 RESULT 185449.5619747 RESULT -54.05979017059 Testing computed result 1.884888131017E+02 against expected result 1.884888E+02 *** PASSED *** Testing computed result 1.820045922544E+03 against expected result 1.820046E+03 *** PASSED *** Testing computed result 6.460002606908E+03 against expected result 6.460003E+03 *** PASSED *** Testing computed result 2.189161497021E+04 against expected result 2.189161E+04 *** PASSED *** Testing computed result 1.520000494925E+05 against expected result 1.520000E+05 *** PASSED *** Testing computed result 1.790436191580E+05 against expected result 1.790436E+05 *** PASSED *** Testing computed result 2.195842512312E+04 against expected result 2.195843E+04 *** PASSED *** Testing computed result 1.537771604355E+05 against expected result 1.537772E+05 *** PASSED *** Testing computed result 1.854495619747E+05 against expected result 1.854496E+05 *** PASSED *** Testing computed result -5.405979017059E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 20.550106 seconds -------------------------------------------------------------------------------- Total elapsed time: 42.559514 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 5823.898055191 RESULT 9793.274462353 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8219.846763777 RESULT 13927.41988698 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3862.359524598 RESULT 6288.15625161 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.67882018629 RESULT -199.7462636633 RESULT -297.4598403628 RESULT -474.5272838398 Testing computed result 5.823898055191E+03 against expected result 5.823898E+03 *** PASSED *** Testing computed result 9.793274462353E+03 against expected result 9.793274E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.219846763777E+03 against expected result 8.219847E+03 *** PASSED *** Testing computed result 1.392741988698E+04 against expected result 1.392742E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.862359524598E+03 against expected result 3.862360E+03 *** PASSED *** Testing computed result 6.288156251610E+03 against expected result 6.288156E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 *** PASSED *** Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 *** PASSED *** Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 *** PASSED *** Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 *** PASSED *** Elapsed time: 5.899850 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 5824.172730822 RESULT 9793.622759239 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8221.328580569 RESULT 13928.67783119 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3863.066835285 RESULT 6289.649216644 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.33052329981 RESULT -198.4883194538 RESULT -295.9668753288 RESULT -472.1246714828 Testing computed result 5.824172730822E+03 against expected result 5.824173E+03 *** PASSED *** Testing computed result 9.793622759239E+03 against expected result 9.793623E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.221328580569E+03 against expected result 8.221329E+03 *** PASSED *** Testing computed result 1.392867783119E+04 against expected result 1.392868E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.863066835285E+03 against expected result 3.863067E+03 *** PASSED *** Testing computed result 6.289649216644E+03 against expected result 6.289649E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 *** PASSED *** Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 *** PASSED *** Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 *** PASSED *** Testing computed result -4.721246714828E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 5.503240 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.403090 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: ion-pmf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.128e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.768e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Checking for intermidiate energies in input file ion-pmf.out RESULT 7839.535983197 RESULT 8964.727588811 RESULT -1125.191605614 RESULT -13.65306965532 Testing computed result 7.839535983197E+03 against expected result 7.839536E+03 *** PASSED *** Testing computed result 8.964727588811E+03 against expected result 8.964728E+03 *** PASSED *** Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 *** PASSED *** Elapsed time: 20.295938 seconds -------------------------------------------------------------------------------- Total elapsed time: 20.295938 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-protein section -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.525554553704E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.967613272771E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050875942181E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.559159533658E+01 kJ/mol Global net ELEC energy = 1.559159533658E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel2.out RESULT 7525.554553704 RESULT 2967.613272771 RESULT 10508.75942181 RESULT 15.59159533658 Testing computed result 7.525554553704E+03 against expected result 7.525555E+03 *** PASSED *** Testing computed result 2.967613272771E+03 against expected result 2.967613E+03 *** PASSED *** Testing computed result 1.050875942181E+04 against expected result 1.050876E+04 *** PASSED *** Testing computed result 1.559159533658E+01 against expected result 1.559160E+01 *** PASSED *** Elapsed time: 32.988814 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.561237446444E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.974076897757E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.055886976547E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 2.355542126539E+01 kJ/mol Global net ELEC energy = 2.355542126539E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel2.out RESULT 7561.237446444 RESULT 2974.076897757 RESULT 10558.86976547 RESULT 23.55542126539 Testing computed result 7.561237446444E+03 against expected result 7.561237E+03 *** PASSED *** Testing computed result 2.974076897757E+03 against expected result 2.974077E+03 *** PASSED *** Testing computed result 1.055886976547E+04 against expected result 1.055887E+04 *** PASSED *** Testing computed result 2.355542126539E+01 against expected result 2.355542E+01 *** PASSED *** Elapsed time: 28.640572 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel12.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.363584355927E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.110802147229E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.892691797082E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.802722643145E+01 kJ/mol Global net ELEC energy = 1.802722643145E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel12.out RESULT 1363.584355927 RESULT 511.0802147229 RESULT 1892.691797082 RESULT 18.02722643145 Testing computed result 1.363584355927E+03 against expected result 1.363584E+03 *** PASSED *** Testing computed result 5.110802147229E+02 against expected result 5.110802E+02 *** PASSED *** Testing computed result 1.892691797082E+03 against expected result 1.892692E+03 *** PASSED *** Testing computed result 1.802722643145E+01 against expected result 1.802723E+01 *** PASSED *** Elapsed time: 24.679346 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel12.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.366571366426E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.108315415905E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.896685358215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.928245019843E+01 kJ/mol Global net ELEC energy = 1.928245019843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel12.out RESULT 1366.571366426 RESULT 510.8315415905 RESULT 1896.685358215 RESULT 19.28245019843 Testing computed result 1.366571366426E+03 against expected result 1.366571E+03 *** PASSED *** Testing computed result 5.108315415905E+02 against expected result 5.108315E+02 *** PASSED *** Testing computed result 1.896685358215E+03 against expected result 1.896685E+03 *** PASSED *** Testing computed result 1.928245019843E+01 against expected result 1.928245E+01 *** PASSED *** Elapsed time: 26.250663 seconds -------------------------------------------------------------------------------- Total elapsed time: 112.559395 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-vdw.out RESULT 2224.988750664 RESULT 10496.95084686 RESULT 181845.0789522 RESULT 300825.4338259 RESULT 184091.8409896 RESULT 311330.4681884 RESULT 8.083515648803 Testing computed result 2.224988750664E+03 against expected result 2.224989E+03 *** PASSED *** Testing computed result 1.049695084686E+04 against expected result 1.049695E+04 *** PASSED *** Testing computed result 1.818450789522E+05 against expected result 1.818451E+05 *** PASSED *** Testing computed result 3.008254338259E+05 against expected result 3.008254E+05 *** PASSED *** Testing computed result 1.840918409896E+05 against expected result 1.840918E+05 *** PASSED *** Testing computed result 3.113304681884E+05 against expected result 3.113305E+05 *** PASSED *** Testing computed result 8.083515648803E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 31.450215 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-vdw.out RESULT 2226.793167046 RESULT 10505.04485887 RESULT 182797.6621645 RESULT 301722.8546773 RESULT 185081.9075387 RESULT 312248.8625388 RESULT 20.9630025572 Testing computed result 2.226793167046E+03 against expected result 2.226793E+03 *** PASSED *** Testing computed result 1.050504485887E+04 against expected result 1.050504E+04 *** PASSED *** Testing computed result 1.827976621645E+05 against expected result 1.827977E+05 *** PASSED *** Testing computed result 3.017228546773E+05 against expected result 3.017229E+05 *** PASSED *** Testing computed result 1.850819075387E+05 against expected result 1.850819E+05 *** PASSED *** Testing computed result 3.122488625388E+05 against expected result 3.122489E+05 *** PASSED *** Testing computed result 2.096300255720E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 27.560217 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-surf.out RESULT 2244.350164274 RESULT 10521.49475373 RESULT 186261.5690066 RESULT 305181.0884053 RESULT 188662.5455219 RESULT 315821.8439277 RESULT 119.2607686582 Testing computed result 2.244350164274E+03 against expected result 2.244350E+03 *** PASSED *** Testing computed result 1.052149475373E+04 against expected result 1.052149E+04 *** PASSED *** Testing computed result 1.862615690066E+05 against expected result 1.862616E+05 *** PASSED *** Testing computed result 3.051810884053E+05 against expected result 3.051811E+05 *** PASSED *** Testing computed result 1.886625455219E+05 against expected result 1.886625E+05 *** PASSED *** Testing computed result 3.158218439277E+05 against expected result 3.158218E+05 *** PASSED *** Testing computed result 1.192607686582E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 25.129966 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-surf.out RESULT 2251.46678942 RESULT 10528.14502873 RESULT 186407.1689626 RESULT 305331.9953673 RESULT 188802.7142979 RESULT 315969.0177241 RESULT 108.8773280806 Testing computed result 2.251466789420E+03 against expected result 2.251467E+03 *** PASSED *** Testing computed result 1.052814502873E+04 against expected result 1.052815E+04 *** PASSED *** Testing computed result 1.864071689626E+05 against expected result 1.864072E+05 *** PASSED *** Testing computed result 3.053319953673E+05 against expected result 3.053320E+05 *** PASSED *** Testing computed result 1.888027142979E+05 against expected result 1.888027E+05 *** PASSED *** Testing computed result 3.159690177241E+05 against expected result 3.159690E+05 *** PASSED *** Testing computed result 1.088773280806E+02 against expected result 1.088773E+02 *** PASSED *** Elapsed time: 22.969839 seconds -------------------------------------------------------------------------------- Total elapsed time: 107.110237 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_1.out RESULT 97.76035707281 RESULT 89.75920687031 RESULT 205.8277719334 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 89.7592 RESULT 205.828 RESULT 96.5336 RESULT 88.6151 RESULT 201.106 RESULT 18.30820799027 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 8.975920687031E+01 against expected result 8.975921E+01 *** PASSED *** Testing computed result 2.058277719334E+02 against expected result 2.058278E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 8.975920000000E+01 against expected result 8.975920E+01 *** PASSED *** Testing computed result 2.058280000000E+02 against expected result 2.058280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 8.861510000000E+01 against expected result 8.861510E+01 *** PASSED *** Testing computed result 2.011060000000E+02 against expected result 2.011060E+02 *** PASSED *** Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 *** PASSED *** Elapsed time: 1.379327 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_2.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 208.4282010393 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 208.428 RESULT 96.5336 RESULT 100.656 RESULT 203.83 RESULT 8.906694086751 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.084282010393E+02 against expected result 2.084282E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.084280000000E+02 against expected result 2.084280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006560000000E+02 against expected result 1.006560E+02 *** PASSED *** Testing computed result 2.038300000000E+02 against expected result 2.038300E+02 *** PASSED *** Testing computed result 8.906694086751E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 1.260063 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_3.out RESULT 97.76035707281 RESULT 133.7661883222 RESULT 237.436145212 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 133.766 RESULT 237.436 RESULT 96.5336 RESULT 132.672 RESULT 232.924 RESULT 5.909599816984 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.337661883222E+02 against expected result 1.337662E+02 *** PASSED *** Testing computed result 2.374361452120E+02 against expected result 2.374361E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.337660000000E+02 against expected result 1.337660E+02 *** PASSED *** Testing computed result 2.374360000000E+02 against expected result 2.374360E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.326720000000E+02 against expected result 1.326720E+02 *** PASSED *** Testing computed result 2.329240000000E+02 against expected result 2.329240E+02 *** PASSED *** Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 *** PASSED *** Elapsed time: 1.246276 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_4.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 203.9516519 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 203.952 RESULT 96.5336 RESULT 100.654 RESULT 199.493 RESULT 4.430144947418 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.039516519000E+02 against expected result 2.039517E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.039520000000E+02 against expected result 2.039520E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006540000000E+02 against expected result 1.006540E+02 *** PASSED *** Testing computed result 1.994930000000E+02 against expected result 1.994930E+02 *** PASSED *** Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 *** PASSED *** Elapsed time: 1.353595 seconds -------------------------------------------------------------------------------- Total elapsed time: 5.239261 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 1847.663548071 RESULT 1883.912182952 RESULT 2732.623683321 RESULT 3123.035854133 RESULT -36.24863488075 RESULT -390.4121708125 RESULT -354.1635359318 Testing computed result 1.847663548071E+03 against expected result 1.847664E+03 *** PASSED *** Testing computed result 1.883912182952E+03 against expected result 1.883912E+03 *** PASSED *** Testing computed result 2.732623683321E+03 against expected result 2.732624E+03 *** PASSED *** Testing computed result 3.123035854133E+03 against expected result 3.123036E+03 *** PASSED *** Testing computed result -3.624863488075E+01 against expected result -3.624863E+01 *** PASSED *** Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 *** PASSED *** Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 *** PASSED *** Elapsed time: 1.770182 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 20 2022 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 1847.86044002 RESULT 1885.436377745 RESULT 2734.040568569 RESULT 3125.279428954 RESULT -37.57593772492 RESULT -391.2388603848 RESULT -353.6629226599 Testing computed result 1.847860440020E+03 against expected result 1.847860E+03 *** PASSED *** Testing computed result 1.885436377745E+03 against expected result 1.885436E+03 *** PASSED *** Testing computed result 2.734040568569E+03 against expected result 2.734041E+03 *** PASSED *** Testing computed result 3.125279428954E+03 against expected result 3.125279E+03 *** PASSED *** Testing computed result -3.757593772492E+01 against expected result -3.757594E+01 *** PASSED *** Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 *** PASSED *** Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 *** PASSED *** Elapsed time: 1.959853 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.730035 seconds Test results have been logged -------------------------------------------------------------------------------- Processing files: apbs-3.0.0-16.fc37.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs = 3.0.0-16.fc37 apbs(aarch-64) = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.34)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-tools-3.0.0-16.fc37.aarch64 warning: absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.11/site-packages/apbs/psize.py Provides: apbs-tools = 3.0.0-16.fc37 apbs-tools(aarch-64) = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.34)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-libs-3.0.0-16.fc37.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4si1lm + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-libs + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-libs + cp -pr README.md /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.u3MrIu + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + cp -pr LICENSE.md /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + cp -pr COPYING /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + cp -pr contrib/iapbs/iapbs-COPYING /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + cp -pr contrib/iapbs/iapbs-LGPLv2 /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-libs = 3.0.0-16.fc37 apbs-libs(aarch-64) = 3.0.0-16.fc37 libapbs.so.1()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH) Processing files: apbs-devel-3.0.0-16.fc37.aarch64 Provides: apbs-devel = 3.0.0-16.fc37 apbs-devel(aarch-64) = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) Processing files: apbs-doc-3.0.0-16.fc37.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.cl1uPj + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-doc + cp -pr build/doc /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/doc/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.UPtBbW + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-doc + cp -pr LICENSE.md /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64/usr/share/licenses/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-doc = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-apbs-3.0.0-16.fc37.aarch64 Provides: python-apbs = 3.0.0-16.fc37 python3-apbs = 3.0.0-16.fc37 python3-apbs(aarch-64) = 3.0.0-16.fc37 python3.11-apbs = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/python3 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libmaloc.so.1()(64bit) libpython3.11.so.1.0()(64bit) python(abi) = 3.11 rtld(GNU_HASH) Obsoletes: apbs-libs < 0:3.0.0-11 python-apbs < 3.0.0-16.fc37 Processing files: apbs-debugsource-3.0.0-16.fc37.aarch64 Provides: apbs-debugsource = 3.0.0-16.fc37 apbs-debugsource(aarch-64) = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: apbs-debuginfo-3.0.0-16.fc37.aarch64 Provides: apbs-debuginfo = 3.0.0-16.fc37 apbs-debuginfo(aarch-64) = 3.0.0-16.fc37 debuginfo(build-id) = 42be642e5d6a44a6c528dd15a0c09f8260d8446e Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(aarch-64) = 3.0.0-16.fc37 Processing files: apbs-tools-debuginfo-3.0.0-16.fc37.aarch64 Provides: apbs-tools-debuginfo = 3.0.0-16.fc37 apbs-tools-debuginfo(aarch-64) = 3.0.0-16.fc37 debuginfo(build-id) = 0ac9dbd480dda60ce247ad1701de96fadc4fac4a debuginfo(build-id) = 367b7d4cc48fd74c69f741e956c8cede506c3152 debuginfo(build-id) = 452fec20f3861eb0936d1e49706201f607d622dd debuginfo(build-id) = 482865a0efabce6780388b3842a577a8b8b31ab0 debuginfo(build-id) = 4867c88e3d02d50ccac4ab5cba86de1176d6fd97 debuginfo(build-id) = 5536733fd8aa436ea3be8f0821abb2517fc51419 debuginfo(build-id) = 554c9a82799cce2a5bfcc51a001f299e5bd2f63f debuginfo(build-id) = 5d0c9082350f81db182fa53be45865d90128d48e debuginfo(build-id) = 60505ca4b815c86cacbd242837fbcc525ff55e35 debuginfo(build-id) = 856a64fb098a3a544164911c5bae9c3bbe2aa9bf debuginfo(build-id) = ae8ecbb4e60d99fe455efb09ace60c3df0137107 debuginfo(build-id) = c2f87c2a89ed27d98b8c46ce47377f8339dec10f debuginfo(build-id) = d2331d65caf619b3cccbf144427e64c530ac6fc5 debuginfo(build-id) = eaee5c487eba690a83e48d1e5f457f0acb07313f debuginfo(build-id) = ec4fe27ee5dcc82ea32540c7cadc1702e69aa712 debuginfo(build-id) = eecc7dbf704f5d5b21a4547e133f8d7eb545dcf5 debuginfo(build-id) = fdb88c38e4c7f3a679653952330a94eaa520d164 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(aarch-64) = 3.0.0-16.fc37 Processing files: apbs-libs-debuginfo-3.0.0-16.fc37.aarch64 Provides: apbs-libs-debuginfo = 3.0.0-16.fc37 apbs-libs-debuginfo(aarch-64) = 3.0.0-16.fc37 debuginfo(build-id) = d09d8c529dd49d681115e0a72261bf9105f49456 libapbs.so.1-3.0.0-16.fc37.aarch64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(aarch-64) = 3.0.0-16.fc37 Processing files: python3-apbs-debuginfo-3.0.0-16.fc37.aarch64 Provides: debuginfo(build-id) = f801835527c46d64380330cee7d0ef5b8dd88064 python-apbs-debuginfo = 3.0.0-16.fc37 python3-apbs-debuginfo = 3.0.0-16.fc37 python3-apbs-debuginfo(aarch-64) = 3.0.0-16.fc37 python3.11-apbs-debuginfo = 3.0.0-16.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(aarch-64) = 3.0.0-16.fc37 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 Wrote: /builddir/build/RPMS/apbs-tools-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-libs-debuginfo-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/python3-apbs-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/python3-apbs-debuginfo-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-libs-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-devel-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-debuginfo-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-tools-debuginfo-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-debugsource-3.0.0-16.fc37.aarch64.rpm Wrote: /builddir/build/RPMS/apbs-doc-3.0.0-16.fc37.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.w5bCa9 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-16.fc37.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.CNsBUQ + umask 022 + cd /builddir/build/BUILD + rm -rf apbs-3.0.0 apbs-3.0.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.11/site-packages/apbs/psize.py Child return code was: 0