Hello community, here is the log from the commit of package votca-csg for openSUSE:Factory checked in at 2020-06-23 21:05:28 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/votca-csg (Old) and /work/SRC/openSUSE:Factory/.votca-csg.new.2956 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-csg" Tue Jun 23 21:05:28 2020 rev:17 rq:816421 version:1.6.1 Changes: -------- --- /work/SRC/openSUSE:Factory/votca-csg/votca-csg.changes 2020-06-15 20:27:32.801758267 +0200 +++ /work/SRC/openSUSE:Factory/.votca-csg.new.2956/votca-csg.changes 2020-06-23 21:05:50.998085594 +0200 @@ -1,0 +2,14 @@ +Mon Jun 22 12:18:02 UTC 2020 - Christoph Junghans <[email protected]> + +- Update to 1.6.1 + - add support for cma-3 ([gh#votca/csg#158]) + - allow special characters in build directory + ([gh#votca/csg#521]) + - fix CI on Ubuntu-20.04 ([gh#votca/csg#526]) + - drop support for gmx 2016 ([gh#votca/csg#529], + [gh#votca/csg#547]) + - fix csg_reupdate and add tests ([gh#votca/csg#525]) + - fix detection of lmp and gmx in cmake ([gh#votca/csg#540]) + - add test for lammpsdata reader ([gh#votca/csg#544]) + +------------------------------------------------------------------- Old: ---- votca-csg-1.6.tar.gz votca-csg-manual-1.6.pdf votca-csg-tutorials-1.6.tar.gz New: ---- votca-csg-1.6.1.tar.gz votca-csg-manual-1.6.1.pdf votca-csg-tutorials-1.6.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ votca-csg.spec ++++++ --- /var/tmp/diff_new_pack.YiHMi0/_old 2020-06-23 21:05:51.634087649 +0200 +++ /var/tmp/diff_new_pack.YiHMi0/_new 2020-06-23 21:05:51.634087649 +0200 @@ -18,7 +18,7 @@ Name: votca-csg -Version: 1.6 +Version: 1.6.1 Release: 0 %define uversion %{version} %define sover 6 ++++++ votca-csg-1.6.tar.gz -> votca-csg-1.6.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/.gitlab-ci.yml new/csg-1.6.1/.gitlab-ci.yml --- old/csg-1.6/.gitlab-ci.yml 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/.gitlab-ci.yml 2020-06-21 15:20:18.000000000 +0200 @@ -37,7 +37,7 @@ - pushd build - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON -DBUILD_CSG_MANUAL=ON -DENABLE_WERROR=ON -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_REGRESSION_TESTING=${REGRESSION_TESTING:-ON} - -DBUILD_OWN_GROMACS=${BUILD_GROMACS} ${BUILD_GROMACS:+-DENABLE_WARNING_FLAGS=OFF} + -DBUILD_OWN_GROMACS=${BUILD_GROMACS} ${BUILD_GROMACS:+-DENABLE_WARNING_FLAGS=OFF -DENABLE_WERROR=OFF} -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install} ${MINIMAL:+-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON -DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=ON -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DBUILD_MANPAGES=OFF -DWITH_GMX=OFF -DBUILD_XTP=OFF -DENABLE_REGRESSION_TESTING=OFF} @@ -106,6 +106,7 @@ CXX: "g++" CMAKE_BUILD_TYPE: "Debug" DISTRO: "ubuntu" + REGRESSION_TESTING: "OFF" extends: .build Debug Clang Ubuntu: @@ -114,6 +115,7 @@ CXX: "clang++" CMAKE_BUILD_TYPE: "Debug" DISTRO: "ubuntu" + REGRESSION_TESTING: "OFF" extends: .build Release GCC Ubuntu: @@ -122,6 +124,7 @@ CXX: "g++" CMAKE_BUILD_TYPE: "Release" DISTRO: "ubuntu" + REGRESSION_TESTING: "OFF" extends: .build Release Clang Ubuntu: @@ -130,6 +133,7 @@ CXX: "clang++" CMAKE_BUILD_TYPE: "Release" DISTRO: "ubuntu" + REGRESSION_TESTING: "OFF" extends: .build Debug GCC Rawhide: @@ -194,70 +198,6 @@ MODULE_BUILD: "yes" extends: .build -Release GCC GMX2016: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016" - extends: .build - -Release Clang GMX2016: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016" - extends: .build - -Release GCC GMX2016D: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016_d" - extends: .build - -Release Clang GMX2016D: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016_d" - extends: .build - -Release GCC GMX2018: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018" - extends: .build - -Release Clang GMX2018: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018" - extends: .build - -Release GCC GMX2018D: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018_d" - extends: .build - -Release Clang GMX2018D: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018_d" - extends: .build - Release GCC GMX2019: variables: CC: "gcc" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/CHANGELOG.md new/csg-1.6.1/CHANGELOG.md --- old/csg-1.6/CHANGELOG.md 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/CHANGELOG.md 2020-06-21 15:20:18.000000000 +0200 @@ -1,6 +1,15 @@ For more detailed information about the changes see the history of the [repository](https://github.com/votca/csg/commits/master). +## Version 1.6.1 (released 21.06.20) +* add support for cma-3 (#158) +* allow special characters in build directory (#521) +* fix CI on Ubuntu-20.04 (#526) +* drop support for gmx 2016 (#529, #547) +* fix csg_reupdate and add tests (#525) +* fix detection of lmp and gmx in cmake (#540) +* add test for lammpsdata reader (#544) + ## Version 1.6 _SuperPelagia_ (released 17.04.20) * enforce periodic boundaries for dihedrals (#500) * add warning about dihedrals (#500) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/CMakeLists.txt new/csg-1.6.1/CMakeLists.txt --- old/csg-1.6/CMakeLists.txt 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/CMakeLists.txt 2020-06-21 15:20:18.000000000 +0200 @@ -2,7 +2,7 @@ project(votca-csg) -set(PROJECT_VERSION "1.6") +set(PROJECT_VERSION "1.6.1") set(PROJECT_CONTACT "[email protected]") string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}") if (NOT ${SOVERSION} MATCHES "[1-9]+") @@ -75,14 +75,14 @@ if (WITH_GMX) find_package(GROMACS 2021 QUIET CONFIG NAMES gromacs gromacs_d) if(NOT GROMACS_FOUND) - find_package(GROMACS 2016 REQUIRED MODULE) + find_package(GROMACS 2018 REQUIRED MODULE) endif() if(DEFINED GROMACS_VERSION AND GROMACS_VERSION VERSION_GREATER_EQUAL "2020") message(WARNING "Gromacs-2020 and above have no support for tabulated interactions, that are needed for coarse-graining (see and comment on https://gitlab.com/gromacs/gromacs/-/issues/1347)") endif() endif(WITH_GMX) -find_program(GMX_EXECUTABLE gmx_d gmx) +find_program(GMX_EXECUTABLE NAMES gmx_d gmx) find_package_handle_standard_args(GMX REQUIRED_VARS GMX_EXECUTABLE) if(ENABLE_TESTING) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/scripts/CMakeLists.txt new/csg-1.6.1/scripts/CMakeLists.txt --- old/csg-1.6/scripts/CMakeLists.txt 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/scripts/CMakeLists.txt 2020-06-21 15:20:18.000000000 +0200 @@ -22,7 +22,7 @@ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT} DESTINATION ${CMAKE_INSTALL_BINDIR}) if (TXT2TAGS_FOUND AND BASH) add_custom_command(OUTPUT ${SCRIPT}.man - COMMAND VOTCASHARE=${CMAKE_SOURCE_DIR}/share ${BASH} ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT} --help > ${SCRIPT}.help + COMMAND ${CMAKE_COMMAND} -E env VOTCASHARE=${CMAKE_SOURCE_DIR}/share ${BASH} ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT} --help > ${SCRIPT}.help COMMAND ${BASH} ${CMAKE_CURRENT_BINARY_DIR}/help2t2t ${SCRIPT}.help > ${SCRIPT}.t2t COMMAND ${TXT2TAGS_EXECUTABLE} -q -t man -i ${SCRIPT}.t2t -o ${SCRIPT}.man DEPENDS help2t2t_build ${SCRIPT}) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/share/scripts/inverse/cma_processor.py new/csg-1.6.1/share/scripts/inverse/cma_processor.py --- old/csg-1.6/share/scripts/inverse/cma_processor.py 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/share/scripts/inverse/cma_processor.py 2020-06-21 15:20:18.000000000 +0200 @@ -16,7 +16,7 @@ # -from optparse import OptionParser +import argparse import sys import re import pickle @@ -89,10 +89,11 @@ usage = "usage: %prog [options] statefile-in statefile-out" -parser = OptionParser(usage=usage) -parser.add_option("--eps", dest="eps", metavar="EPS", +parser = argparse.ArgumentParser(description=usage) + +parser.add_argument("--eps", dest="eps", metavar="EPS", type=float, help="tolerance for initialization", default=0.1) -(options, args) = parser.parse_args() +(options, args) = parser.parse_known_args() if len(args) != 2: sys.exit("two statefile required as parameters") diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/share/scripts/inverse/run_genericsim.sh new/csg-1.6.1/share/scripts/inverse/run_genericsim.sh --- old/csg-1.6/share/scripts/inverse/run_genericsim.sh 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/share/scripts/inverse/run_genericsim.sh 2020-06-21 15:20:18.000000000 +0200 @@ -1,6 +1,6 @@ #! /bin/bash # -# Copyright 2009-2013 The VOTCA Development Team (http://www.votca.org) +# Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -40,7 +40,7 @@ echo "${0##*/}: $sim_prog does not support wallclock time yet (go here and implement it). Per step wallclock time check is still performed!" fi -if [[ ${CSG_MDRUN_STEPS} ]]; then +if [[ ${CSG_MDRUN_STEPS} && ! ${CSG_DONT_OVERWRITE_MDRUN_STEPS} ]]; then if [[ ${sim_prog} = "lammps" ]]; then critical sed -i "/^run/s/[0-9][0-9]*/${CSG_MDRUN_STEPS}/" "$script" msg --color blue --to-stderr "Replace run STEPS in '$script' to be ${CSG_MDRUN_STEPS}" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/share/scripts/inverse/run_gromacs.sh new/csg-1.6.1/share/scripts/inverse/run_gromacs.sh --- old/csg-1.6/share/scripts/inverse/run_gromacs.sh 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/share/scripts/inverse/run_gromacs.sh 2020-06-21 15:20:18.000000000 +0200 @@ -1,6 +1,6 @@ #! /bin/bash # -# Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) +# Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -113,7 +113,7 @@ msg "Doing main simulation" fi -if [[ ${CSG_MDRUN_STEPS} ]]; then +if [[ ${CSG_MDRUN_STEPS} && ! ${CSG_DONT_OVERWRITE_MDRUN_STEPS} ]]; then msg --color blue --to-stderr "Appending -nsteps ${CSG_MDRUN_STEPS} to mdrun options" mdrun_opts+=" -nsteps $CSG_MDRUN_STEPS" fi diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/share/xml/CMakeLists.txt new/csg-1.6.1/share/xml/CMakeLists.txt --- old/csg-1.6/share/xml/CMakeLists.txt 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/share/xml/CMakeLists.txt 2020-06-21 15:20:18.000000000 +0200 @@ -10,7 +10,7 @@ if(NOT GMX_FOUND) set(GMX_EXECUTABLE "gmx") endif() -find_program(LMP_EXECUTABLE lmp lammps) +find_program(LMP_EXECUTABLE NAMES lmp lammps) find_package_handle_standard_args(LMP REQUIRED_VARS LMP_EXECUTABLE) if(NOT LMP_FOUND) set(LMP_EXECUTABLE "lmp") diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/libcsg/modules/io/gmxtopologyreader.cc new/csg-1.6.1/src/libcsg/modules/io/gmxtopologyreader.cc --- old/csg-1.6/src/libcsg/modules/io/gmxtopologyreader.cc 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/src/libcsg/modules/io/gmxtopologyreader.cc 2020-06-21 15:20:18.000000000 +0200 @@ -1,5 +1,5 @@ /* - * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) + * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/CMakeLists.txt new/csg-1.6.1/src/tools/CMakeLists.txt --- old/csg-1.6/src/tools/CMakeLists.txt 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/src/tools/CMakeLists.txt 2020-06-21 15:20:18.000000000 +0200 @@ -35,6 +35,43 @@ set_tests_properties(integration_Compare_csg_reupdate_output PROPERTIES DEPENDS integration_Run_csg_reupdate) set_tests_properties(integration_Compare_csg_reupdate_output PROPERTIES LABELS "csg;tools;votca;integration") + + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_reupdate2) + file(MAKE_DIRECTORY ${RUNPATH}) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.rdf ${RUNPATH}/CG-CG.dist.new) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.imc.tgt ${RUNPATH}/CG-CG.dist.tgt) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.param.in_re ${RUNPATH}/CG-CG.param.cur) + add_test(NAME integration_Run_csg_reupdate2 COMMAND csg_reupdate --options ${REFPATH}/settings_re.xml --top ${REFPATH}/topol_cg.xml --trj ${REFPATH}/frame_cg.dump --hessian-check no WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Run_csg_reupdate2 PROPERTIES LABELS "csg;tools;votca") + add_test(NAME integration_Compare_csg_reupdate_output2 COMMAND $<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1 CG-CG.pot.new -f2 ${REFPATH}/CG-CG.pot.new.re WORKING_DIRECTORY ${RUNPATH}) + add_test(NAME integration_Compare_csg_reupdate_output3 COMMAND $<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1 CG-CG.param.new -f2 ${REFPATH}/CG-CG.param.re WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Compare_csg_reupdate_output2 PROPERTIES DEPENDS integration_Run_csg_reupdate2) + set_tests_properties(integration_Compare_csg_reupdate_output2 PROPERTIES LABELS "csg;tools;votca") + set_tests_properties(integration_Compare_csg_reupdate_output3 PROPERTIES DEPENDS integration_Run_csg_reupdate2) + set_tests_properties(integration_Compare_csg_reupdate_output3 PROPERTIES LABELS "csg;tools;votca") + + if(GMX_FOUND) + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_reupdate_gmx) + file(MAKE_DIRECTORY ${RUNPATH}) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/topol_cg.top ${RUNPATH}/topol.top) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/grompp_cg.mdp ${RUNPATH}/grompp.mdp) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/conf_cg.gro ${RUNPATH}/conf.gro) + add_test(NAME integration_Run_gmx_grompp_re COMMAND ${GMX_EXECUTABLE} grompp WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Run_gmx_grompp_re PROPERTIES LABELS "csg;tools;votca;integration") + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.rdf ${RUNPATH}/CG-CG.dist.new) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.imc.tgt ${RUNPATH}/CG-CG.dist.tgt) + execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ${REFPATH}/CG-CG.param.in_re ${RUNPATH}/CG-CG.param.cur) + add_test(NAME integration_Run_csg_reupdate_gmx COMMAND csg_reupdate --options ${REFPATH}/settings_re.xml --top topol.tpr --trj conf.gro --hessian-check no WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Run_csg_reupdate_gmx PROPERTIES DEPENDS integration_Run_gmx_grompp_re) + set_tests_properties(integration_Run_csg_reupdate_gmx PROPERTIES LABELS "csg;tools;votca") + add_test(NAME integration_Compare_csg_reupdate_gmx_output COMMAND $<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1 CG-CG.pot.new -f2 ${REFPATH}/CG-CG.pot.new.re_gmx WORKING_DIRECTORY ${RUNPATH}) + add_test(NAME integration_Compare_csg_reupdate_gmx_output2 COMMAND $<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1 CG-CG.param.new -f2 ${REFPATH}/CG-CG.param.re_gmx WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Compare_csg_reupdate_gmx_output PROPERTIES DEPENDS integration_Run_csg_reupdate_gmx) + set_tests_properties(integration_Compare_csg_reupdate_gmx_output PROPERTIES LABELS "csg;tools;votca") + set_tests_properties(integration_Compare_csg_reupdate_gmx_output2 PROPERTIES DEPENDS integration_Run_csg_reupdate_gmx) + set_tests_properties(integration_Compare_csg_reupdate_gmx_output2 PROPERTIES LABELS "csg;tools;votca") + endif() + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_fmatch) file(MAKE_DIRECTORY ${RUNPATH}) add_test(NAME integration_Run_csg_fmatch @@ -73,6 +110,14 @@ set_tests_properties(integration_Compare_csg_map_output PROPERTIES DEPENDS integration_Run_csg_map) set_tests_properties(integration_Compare_csg_map_output PROPERTIES LABELS "csg;tools;votca;integration") + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_map_gro) + file(MAKE_DIRECTORY ${RUNPATH}) + add_test(NAME integration_Run_csg_map_gro COMMAND csg_map --top ${REFPATH}/topol.xml --trj ${REFPATH}/frame.dump --cg ${REFPATH}/mapping.xml --out conf_cg.gro --nframes 1 WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Run_csg_map_gro PROPERTIES LABELS "csg;tools;votca;integration") + add_test(NAME integration_Compare_csg_map_gro_output COMMAND $<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1 conf_cg.gro -f2 ${REFPATH}/conf_cg.gro WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Compare_csg_map_gro_output PROPERTIES DEPENDS integration_Run_csg_map_gro) + set_tests_properties(integration_Compare_csg_map_gro_output PROPERTIES LABELS "csg;tools;votca;integration") + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_stat) file(MAKE_DIRECTORY ${RUNPATH}) add_test(NAME integration_Run_csg_stat @@ -208,6 +253,17 @@ add_test(NAME integration_Compare_csg_dump_gro_output COMMAND ${CMAKE_COMMAND} -E compare_files csg_dump_gro.out ${REFPATH}/csg_dump_gro.out WORKING_DIRECTORY ${RUNPATH}) set_tests_properties(integration_Compare_csg_dump_gro_output PROPERTIES DEPENDS integration_Run_csg_dump_gro) set_tests_properties(integration_Compare_csg_dump_gro_output PROPERTIES LABELS "csg;tools;votca;integration") + + set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_dump_data) + set(REFPATH ${CMAKE_CURRENT_SOURCE_DIR}/references/spce/3mols_cg) + file(MAKE_DIRECTORY ${RUNPATH}) + add_test(NAME integration_Run_csg_dump_data + COMMAND ${BASH} -c "$<TARGET_FILE:csg_dump> --top ${REFPATH}/spce.data > csg_dump_data.out" + WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Run_csg_dump_data PROPERTIES LABELS "csg;tools;votca;integration") + add_test(NAME integration_Compare_csg_dump_data_output COMMAND ${CMAKE_COMMAND} -E compare_files csg_dump_data.out ${REFPATH}/csg_dump_data.out WORKING_DIRECTORY ${RUNPATH}) + set_tests_properties(integration_Compare_csg_dump_data_output PROPERTIES DEPENDS integration_Run_csg_dump_data) + set_tests_properties(integration_Compare_csg_dump_data_output PROPERTIES LABELS "csg;tools;votca;integration") endif() if(GMX_FOUND) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/csg_reupdate.cc new/csg-1.6.1/src/tools/csg_reupdate.cc --- old/csg-1.6/src/tools/csg_reupdate.cc 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/src/tools/csg_reupdate.cc 2020-06-21 15:20:18.000000000 +0200 @@ -1,5 +1,5 @@ /* - * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) + * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -65,7 +65,7 @@ " Extension of the output potential tables")( "hessian-check", boost::program_options::value<bool>(&_hessian_check)->default_value(true), - " Extension of the output potential tables"); + " Disable the hessian check (mostly for testing)"); AddProgramOptions()("top", boost::program_options::value<string>(), " atomistic topology file (only needed for RE update)"); } @@ -285,17 +285,8 @@ /* adding 4th term in eq. 52 of ref J. Chem. Phys. 134, 094112, 2011 * to _HS */ - for (votca::Index row = 0; row < _nlamda; row++) { - for (votca::Index col = row; col < _nlamda; col++) { - - _HS(row, col) += (-1.0 * _DS(row) * _DS(col)); - _HS(col, row) += (-1.0 * _DS(row) * _DS(col)); - // since at this step _DS(i) = -beta*<dU/dlamda_i>cg - - } // end loop over col - - } // end loop over row + _HS -= _DS * _DS.transpose(); /* adding 1st term (i.e. aa ensemble avg) of eq. 51 to _DS * and of eq. 52 to _DH @@ -452,8 +443,9 @@ } // end loop pair_iter _HS(row, col) += (_beta * d2U_ij); - _HS(col, row) += (_beta * d2U_ij); - + if (row != col) { + _HS(col, row) += (_beta * d2U_ij); + } } // end loop col } // end loop row @@ -635,7 +627,9 @@ } _HS(row, col) -= _beta * d2U_ij; - _HS(col, row) -= _beta * d2U_ij; + if (row != col) { + _HS(col, row) -= _beta * d2U_ij; + } } // end loop col } // end loop row diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/3mols_cg/csg_dump_data.out new/csg-1.6.1/src/tools/references/spce/3mols_cg/csg_dump_data.out --- old/csg-1.6/src/tools/references/spce/3mols_cg/csg_dump_data.out 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/3mols_cg/csg_dump_data.out 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,36 @@ + +WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: +angle +atom +bond +full +molecule + +These styles use the following formats in the atom block: +atom-ID molecule-ID atom-type charge x y z +atom-ID molecule-ID atom-type charge x y z nx ny nz +atom-ID molecule-ID atom-type x y z +atom-ID molecule-ID atom-type x y z nx ny nz +atom-ID atom-type x y z +atom-ID atom-type x y z nx ny nz + +Unable to associate mass 18.01540 with element assuming pseudo atom, assigning name Bead1 . +I have 3 beads in 3 molecules +Boundary Condition: orthorhombic + Box matix: 4.031 0 0 + 0 4.031 0 + 0 0 4.031 + +List of residues: +0 name: DUM id: 0 +1 name: DUM id: 1 +2 name: DUM id: 2 +3 name: DUM id: 3 + +List of molecules: +molecule: 1 Be1 beads: 1 +0 Name Bead1 Type Bead1 Mass 18.0154 Resnr 1 Resname DUM Charge 0 +molecule: 2 Be1 beads: 1 +1 Name Bead1 Type Bead1 Mass 18.0154 Resnr 2 Resname DUM Charge 0 +molecule: 3 Be1 beads: 1 +2 Name Bead1 Type Bead1 Mass 18.0154 Resnr 3 Resname DUM Charge 0 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/3mols_cg/spce.data new/csg-1.6.1/src/tools/references/spce/3mols_cg/spce.data --- old/csg-1.6/src/tools/references/spce/3mols_cg/spce.data 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/3mols_cg/spce.data 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,19 @@ + Coarse-grained water + + 3 atoms + + 1 atom types + + 0.0000000E+00 40.310000000000 xlo xhi + 0.0000000E+00 40.310000000000 ylo yhi + 0.0000000E+00 40.310000000000 zlo zhi + + Masses + +1 18.01540 + + Atoms + +1 1 28.15 5.43 2.37 +2 1 1.89 29.57 17.61 +3 1 8.92 35.56 8.24 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/CG-CG.param.re new/csg-1.6.1/src/tools/references/spce/CG-CG.param.re --- old/csg-1.6/src/tools/references/spce/CG-CG.param.re 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/CG-CG.param.re 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,48 @@ +0 207.445072 o +0.006666666667 202.3708213 o +0.01333333333 197.2965706 o +0.02 192.22232 o +0.02666666667 187.1480693 o +0.03333333333 182.0738186 o +0.04 176.999568 o +0.04666666667 171.9253173 o +0.05333333333 166.8510666 o +0.06 161.776816 o +0.06666666667 156.7025653 o +0.07333333333 151.6283147 o +0.08 146.554064 o +0.08666666667 141.4798133 o +0.09333333333 136.4055627 o +0.1 131.331312 o +0.1066666667 126.2570613 o +0.1133333333 121.1828107 o +0.12 116.10856 o +0.1266666667 111.0343094 o +0.1333333333 105.9600587 o +0.14 100.885808 o +0.1466666667 95.81155736 o +0.1533333333 90.7373067 o +0.16 85.66305604 o +0.1666666667 80.58880538 o +0.1733333333 75.51455471 o +0.18 70.44030405 o +0.1866666667 65.36605339 o +0.1933333333 60.29180272 o +0.2 55.21755206 o +0.2066666667 50.1433014 o +0.2133333333 45.06905073 o +0.22 39.99480007 o +0.2266666667 34.92054941 o +0.2333333333 29.84629875 o +0.24 24.77204808 o +0.2466666667 19.69779742 o +0.2533333333 14.62354676 o +0.26 9.549296093 o +0.2666666667 4.47504543 o +0.2733333333 9.549296093 o +0.28 15.72186267 o +0.2866666667 15.48932122 i +0.2933333333 0 i +0.3 0 i +0.3066666667 0 i +0.3133333333 0 i diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/CG-CG.param.re_gmx new/csg-1.6.1/src/tools/references/spce/CG-CG.param.re_gmx --- old/csg-1.6/src/tools/references/spce/CG-CG.param.re_gmx 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/CG-CG.param.re_gmx 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,48 @@ +0 204.2206094 o +0.006666666667 199.2263154 o +0.01333333333 194.2320214 o +0.02 189.2377274 o +0.02666666667 184.2434334 o +0.03333333333 179.2491395 o +0.04 174.2548455 o +0.04666666667 169.2605515 o +0.05333333333 164.2662575 o +0.06 159.2719635 o +0.06666666667 154.2776695 o +0.07333333333 149.2833756 o +0.08 144.2890816 o +0.08666666667 139.2947876 o +0.09333333333 134.3004936 o +0.1 129.3061996 o +0.1066666667 124.3119056 o +0.1133333333 119.3176117 o +0.12 114.3233177 o +0.1266666667 109.3290237 o +0.1333333333 104.3347297 o +0.14 99.34043573 o +0.1466666667 94.34614174 o +0.1533333333 89.35184776 o +0.16 84.35755378 o +0.1666666667 79.3632598 o +0.1733333333 74.36896581 o +0.18 69.37467183 o +0.1866666667 64.38037785 o +0.1933333333 59.38608386 o +0.2 54.39178988 o +0.2066666667 49.3974959 o +0.2133333333 44.40320191 o +0.22 39.40890793 o +0.2266666667 34.41461395 o +0.2333333333 29.42031996 o +0.24 24.42602598 o +0.2466666667 19.431732 o +0.2533333333 14.43743801 o +0.26 9.44314403 o +0.2666666667 4.448850046 o +0.2733333333 9.44314403 o +0.28 15.78700801 o +0.2866666667 15.43989127 i +0.2933333333 0 i +0.3 0 i +0.3066666667 0 i +0.3133333333 0 i diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/CG-CG.pot.new.re new/csg-1.6.1/src/tools/references/spce/CG-CG.pot.new.re --- old/csg-1.6/src/tools/references/spce/CG-CG.pot.new.re 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/CG-CG.pot.new.re 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,21 @@ +0.1 126.2570613 i +0.11 118.6456853 i +0.12 111.0343094 i +0.13 103.4229334 i +0.14 95.81155736 i +0.15 88.20018137 i +0.16 80.58880538 i +0.17 72.97742938 i +0.18 65.36605339 i +0.19 57.75467739 i +0.2 50.1433014 i +0.21 42.5319254 i +0.22 34.92054941 i +0.23 27.30917341 i +0.24 19.69779742 i +0.25 12.08642142 i +0.26 6.166462318 i +0.27 12.52502121 i +0.28 12.94652459 i +0.29 0.3226941921 i +0.3 0 i diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/CG-CG.pot.new.re_gmx new/csg-1.6.1/src/tools/references/spce/CG-CG.pot.new.re_gmx --- old/csg-1.6/src/tools/references/spce/CG-CG.pot.new.re_gmx 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/CG-CG.pot.new.re_gmx 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,21 @@ +0.1 124.3119056 i +0.11 116.8204647 i +0.12 109.3290237 i +0.13 101.8375827 i +0.14 94.34614174 i +0.15 86.85470077 i +0.16 79.3632598 i +0.17 71.87181882 i +0.18 64.38037785 i +0.19 56.88893687 i +0.2 49.3974959 i +0.21 41.90605492 i +0.22 34.41461395 i +0.23 26.92317297 i +0.24 19.431732 i +0.25 11.94029102 i +0.26 6.113614707 i +0.27 12.50379663 i +0.28 12.92442885 i +0.29 0.3216644015 i +0.3 0 i diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/conf_cg.gro new/csg-1.6.1/src/tools/references/spce/conf_cg.gro --- old/csg-1.6/src/tools/references/spce/conf_cg.gro 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/conf_cg.gro 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,219 @@ +what a nice title + 216 + 1SOL CG 1 0.195 0.678 0.192 + 2SOL CG 2 0.202 0.263 1.018 + 3SOL CG 3 1.818 0.389 0.649 + 4SOL CG 4 0.568 1.315 1.198 + 5SOL CG 5 1.615 1.522 0.679 + 6SOL CG 6 1.758 0.601 0.856 + 7SOL CG 7 1.127 0.734 0.690 + 8SOL CG 8 1.781 0.575 0.196 + 9SOL CG 9 0.701 1.133 1.037 + 10SOL CG 10 0.878 0.768 0.007 + 11SOL CG 11 0.715 0.955 0.671 + 12SOL CG 12 0.718 1.178 1.849 + 13SOL CG 13 0.349 1.377 1.048 + 14SOL CG 14 1.477 1.542 1.445 + 15SOL CG 15 0.447 0.387 1.486 + 16SOL CG 16 1.563 0.409 0.779 + 17SOL CG 17 0.265 1.742 0.442 + 18SOL CG 18 1.148 1.345 1.654 + 19SOL CG 19 0.245 1.468 0.519 + 20SOL CG 20 0.313 1.068 0.888 + 21SOL CG 21 0.575 1.784 1.466 + 22SOL CG 22 0.553 1.069 0.177 + 23SOL CG 23 1.540 0.168 1.443 + 24SOL CG 24 0.113 0.673 0.587 + 25SOL CG 25 0.011 1.746 0.314 + 26SOL CG 26 0.025 1.588 0.087 + 27SOL CG 27 1.727 0.935 0.647 + 28SOL CG 28 1.676 1.129 0.438 + 29SOL CG 29 0.081 0.802 1.575 + 30SOL CG 30 0.626 1.388 0.724 + 31SOL CG 31 1.308 1.239 1.384 + 32SOL CG 32 0.827 0.020 0.551 + 33SOL CG 33 0.186 0.948 1.301 + 34SOL CG 34 1.547 1.038 0.207 + 35SOL CG 35 1.223 1.817 1.623 + 36SOL CG 36 0.362 0.222 1.821 + 37SOL CG 37 1.432 1.446 0.897 + 38SOL CG 38 1.705 1.839 0.584 + 39SOL CG 39 0.588 0.724 0.287 + 40SOL CG 40 1.275 0.381 0.956 + 41SOL CG 41 1.613 1.647 0.346 + 42SOL CG 42 0.805 0.596 1.469 + 43SOL CG 43 1.419 0.482 1.668 + 44SOL CG 44 0.942 0.853 1.612 + 45SOL CG 45 1.006 0.392 1.186 + 46SOL CG 46 1.045 0.721 0.427 + 47SOL CG 47 0.077 0.792 0.839 + 48SOL CG 48 0.079 0.010 1.590 + 49SOL CG 49 0.862 0.345 0.228 + 50SOL CG 50 1.675 0.574 1.807 + 51SOL CG 51 1.400 1.156 0.486 + 52SOL CG 52 0.562 0.163 0.983 + 53SOL CG 53 1.002 1.467 0.486 + 54SOL CG 54 0.361 1.809 0.932 + 55SOL CG 55 1.784 1.040 0.895 + 56SOL CG 56 1.203 1.570 1.485 + 57SOL CG 57 0.293 0.914 0.265 + 58SOL CG 58 1.490 0.786 0.748 + 59SOL CG 59 0.474 1.283 1.743 + 60SOL CG 60 1.126 1.788 0.197 + 61SOL CG 61 0.212 0.271 1.543 + 62SOL CG 62 1.622 1.354 0.102 + 63SOL CG 63 0.508 1.786 0.292 + 64SOL CG 64 1.427 0.073 0.458 + 65SOL CG 65 0.265 1.804 1.187 + 66SOL CG 66 0.991 1.682 0.877 + 67SOL CG 67 0.384 0.658 0.470 + 68SOL CG 68 1.512 0.238 1.750 + 69SOL CG 69 0.654 0.138 0.077 + 70SOL CG 70 0.795 0.261 1.737 + 71SOL CG 71 0.870 1.521 1.174 + 72SOL CG 72 1.324 0.604 1.435 + 73SOL CG 73 0.807 1.336 0.905 + 74SOL CG 74 0.941 0.490 0.878 + 75SOL CG 75 0.577 0.087 0.498 + 76SOL CG 76 1.393 1.214 0.040 + 77SOL CG 77 0.303 0.056 0.172 + 78SOL CG 78 0.984 0.267 0.456 + 79SOL CG 79 1.064 0.688 1.439 + 80SOL CG 80 1.228 1.594 0.776 + 81SOL CG 81 0.504 1.121 0.695 + 82SOL CG 82 1.235 1.821 0.627 + 83SOL CG 83 1.035 0.514 0.034 + 84SOL CG 84 0.110 0.600 1.372 + 85SOL CG 85 0.547 0.216 1.229 + 86SOL CG 86 0.854 0.447 0.638 + 87SOL CG 87 1.011 0.072 0.741 + 88SOL CG 88 1.424 1.172 0.819 + 89SOL CG 89 1.430 0.619 0.950 + 90SOL CG 90 1.815 0.776 0.388 + 91SOL CG 91 0.491 1.404 0.163 + 92SOL CG 92 1.746 1.270 0.651 + 93SOL CG 93 1.338 0.546 0.093 + 94SOL CG 94 0.531 0.287 0.283 + 95SOL CG 95 1.727 1.269 1.530 + 96SOL CG 96 1.011 1.335 1.359 + 97SOL CG 97 1.604 1.641 1.694 + 98SOL CG 98 1.150 1.289 1.128 + 99SOL CG 99 1.566 1.099 1.063 + 100SOL CG 100 0.917 0.103 1.349 + 101SOL CG 101 0.979 1.145 1.683 + 102SOL CG 102 0.716 0.997 0.409 + 103SOL CG 103 0.439 0.829 1.262 + 104SOL CG 104 1.251 0.374 1.309 + 105SOL CG 105 0.077 1.577 1.347 + 106SOL CG 106 0.319 1.095 0.448 + 107SOL CG 107 0.539 0.508 0.862 + 108SOL CG 108 1.243 1.354 0.430 + 109SOL CG 109 1.356 1.472 1.167 + 110SOL CG 110 1.503 0.644 0.476 + 111SOL CG 111 0.350 1.540 1.276 + 112SOL CG 112 0.461 0.666 1.603 + 113SOL CG 113 1.644 0.795 1.663 + 114SOL CG 114 1.044 0.126 1.747 + 115SOL CG 115 0.475 1.842 1.774 + 116SOL CG 116 0.588 0.866 1.040 + 117SOL CG 117 1.259 0.875 0.964 + 118SOL CG 118 1.153 0.519 0.284 + 119SOL CG 119 0.268 0.191 1.287 + 120SOL CG 120 0.028 1.318 1.246 + 121SOL CG 121 0.728 0.607 1.035 + 122SOL CG 122 1.755 0.947 0.009 + 123SOL CG 123 0.348 0.037 0.664 + 124SOL CG 124 1.615 0.440 0.367 + 125SOL CG 125 1.029 0.727 0.961 + 126SOL CG 126 0.996 1.581 1.735 + 127SOL CG 127 1.827 1.536 1.598 + 128SOL CG 128 0.355 0.865 1.763 + 129SOL CG 129 1.482 0.318 0.144 + 130SOL CG 130 1.296 0.802 1.856 + 131SOL CG 131 1.072 1.360 0.834 + 132SOL CG 132 0.345 0.791 0.942 + 133SOL CG 133 0.314 0.501 0.993 + 134SOL CG 134 0.469 0.459 1.797 + 135SOL CG 135 1.170 0.377 1.698 + 136SOL CG 136 1.146 0.199 1.470 + 137SOL CG 137 0.011 1.267 0.208 + 138SOL CG 138 0.056 1.743 0.956 + 139SOL CG 139 0.490 1.564 0.886 + 140SOL CG 140 0.936 0.769 1.210 + 141SOL CG 141 0.025 0.541 1.117 + 142SOL CG 142 0.196 0.627 1.777 + 143SOL CG 143 1.394 0.913 1.626 + 144SOL CG 144 0.815 0.583 0.358 + 145SOL CG 145 1.612 0.592 1.154 + 146SOL CG 146 0.232 1.510 1.725 + 147SOL CG 147 0.747 0.434 1.244 + 148SOL CG 148 0.914 1.702 1.488 + 149SOL CG 149 0.429 0.542 0.191 + 150SOL CG 150 0.112 1.136 1.482 + 151SOL CG 151 1.235 1.036 1.176 + 152SOL CG 152 1.359 0.810 0.303 + 153SOL CG 153 1.776 1.682 1.172 + 154SOL CG 154 1.253 1.707 1.071 + 155SOL CG 155 0.114 1.210 0.995 + 156SOL CG 156 0.761 1.673 1.803 + 157SOL CG 157 0.914 0.077 0.119 + 158SOL CG 158 1.766 0.209 0.447 + 159SOL CG 159 1.411 1.553 0.507 + 160SOL CG 160 0.162 1.779 1.840 + 161SOL CG 161 1.297 0.941 0.604 + 162SOL CG 162 0.740 1.287 1.437 + 163SOL CG 163 0.676 1.601 0.180 + 164SOL CG 164 1.619 1.769 1.396 + 165SOL CG 165 1.841 0.121 0.994 + 166SOL CG 166 0.202 0.271 0.693 + 167SOL CG 167 1.198 1.557 0.058 + 168SOL CG 168 0.845 1.030 1.411 + 169SOL CG 169 0.947 0.938 0.273 + 170SOL CG 170 1.492 1.611 0.101 + 171SOL CG 171 0.345 1.305 1.503 + 172SOL CG 172 1.592 1.305 1.265 + 173SOL CG 173 1.128 1.095 0.765 + 174SOL CG 174 0.996 0.243 0.950 + 175SOL CG 175 0.628 1.470 0.460 + 176SOL CG 176 1.765 0.389 1.401 + 177SOL CG 177 0.246 1.327 0.297 + 178SOL CG 178 0.131 1.036 1.726 + 179SOL CG 179 0.690 0.183 1.462 + 180SOL CG 180 0.108 0.355 1.789 + 181SOL CG 181 1.384 0.870 1.362 + 182SOL CG 182 0.055 0.167 0.207 + 183SOL CG 183 1.165 1.292 0.159 + 184SOL CG 184 0.661 0.816 1.433 + 185SOL CG 185 1.504 1.822 1.083 + 186SOL CG 186 0.729 0.560 1.740 + 187SOL CG 187 1.458 1.197 1.611 + 188SOL CG 188 0.306 1.716 1.564 + 189SOL CG 189 1.606 0.866 1.226 + 190SOL CG 190 1.263 0.319 0.462 + 191SOL CG 191 0.614 0.681 0.637 + 192SOL CG 192 1.748 0.317 1.651 + 193SOL CG 193 1.742 0.938 1.458 + 194SOL CG 194 0.874 1.356 0.106 + 195SOL CG 195 0.659 1.771 0.877 + 196SOL CG 196 1.448 1.838 1.794 + 197SOL CG 197 0.902 0.947 0.886 + 198SOL CG 198 1.108 0.979 0.040 + 199SOL CG 199 1.836 1.521 0.846 + 200SOL CG 200 0.178 1.267 1.854 + 201SOL CG 201 0.144 1.199 0.651 + 202SOL CG 202 0.684 1.474 1.632 + 203SOL CG 203 1.811 0.159 1.262 + 204SOL CG 204 0.418 0.395 0.534 + 205SOL CG 205 1.654 1.468 1.053 + 206SOL CG 206 0.376 0.561 1.283 + 207SOL CG 207 0.823 1.614 0.644 + 208SOL CG 208 1.417 0.232 1.137 + 209SOL CG 209 1.014 1.849 1.103 + 210SOL CG 210 0.807 1.271 0.361 + 211SOL CG 211 0.620 1.580 1.285 + 212SOL CG 212 1.367 0.057 0.200 + 213SOL CG 213 1.280 0.481 0.693 + 214SOL CG 214 1.595 0.185 0.933 + 215SOL CG 215 0.041 1.018 0.322 + 216SOL CG 216 0.868 1.683 0.341 + 1.86206 1.86206 1.86206 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/frame_cg.dump new/csg-1.6.1/src/tools/references/spce/frame_cg.dump --- old/csg-1.6/src/tools/references/spce/frame_cg.dump 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/frame_cg.dump 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,225 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +216 +ITEM: BOX BOUNDS pp pp pp +0 18.620600 +0 18.620600 +0 18.620600 +ITEM: ATOMS id type x y z +1 0 1.954941 6.778713 1.918170 +2 0 2.024728 2.625807 10.181598 +3 0 18.178678 3.889877 6.491552 +4 0 5.678828 13.152352 11.978421 +5 0 16.148942 15.224084 6.785547 +6 0 17.581448 6.008219 8.564228 +7 0 11.266224 7.338817 6.902246 +8 0 17.809349 5.750828 1.957666 +9 0 7.008257 11.327640 10.374922 +10 0 8.781554 7.675103 0.074578 +11 0 7.152516 9.551685 6.708429 +12 0 7.183798 11.780242 18.488975 +13 0 3.494191 13.767143 10.483517 +14 0 14.767547 15.420299 14.447281 +15 0 4.472894 3.871705 14.860018 +16 0 15.627565 4.088389 7.792688 +17 0 2.654273 17.424291 4.424575 +18 0 11.481765 13.449472 16.535681 +19 0 2.453287 14.682558 5.186594 +20 0 3.132156 10.678027 8.882078 +21 0 5.745906 17.842461 14.664871 +22 0 5.530844 10.687652 1.769021 +23 0 15.399726 1.683509 14.430261 +24 0 1.131414 6.728364 5.865824 +25 0 0.107216 17.456917 3.144962 +26 0 0.251918 15.883912 0.872264 +27 0 17.267663 9.350678 6.473935 +28 0 16.762646 11.293388 4.378659 +29 0 0.807872 8.017023 15.748572 +30 0 6.262986 13.880848 7.238303 +31 0 13.083722 12.387112 13.842311 +32 0 8.274691 0.197592 5.512270 +33 0 1.861043 9.481968 13.008819 +34 0 15.465769 10.379970 2.065609 +35 0 12.228414 18.170263 16.229849 +36 0 3.615755 2.218067 18.209340 +37 0 14.319637 14.455853 8.974668 +38 0 17.054422 18.392993 5.839697 +39 0 5.880618 7.236378 2.867027 +40 0 12.752861 3.807102 9.562152 +41 0 16.127637 16.473864 3.459455 +42 0 8.051081 5.962818 14.686012 +43 0 14.190564 4.824853 16.676331 +44 0 9.417576 8.527351 16.124430 +45 0 10.059450 3.924566 11.861175 +46 0 10.446666 7.205938 4.270522 +47 0 0.769714 7.922329 8.391524 +48 0 0.791115 0.098438 15.895924 +49 0 8.621992 3.453418 2.282572 +50 0 16.749343 5.743845 18.070947 +51 0 13.998377 11.557987 4.856184 +52 0 5.619869 1.625128 9.826173 +53 0 10.023816 14.669473 4.857171 +54 0 3.609156 18.088702 9.316211 +55 0 17.835301 10.397842 8.947877 +56 0 12.025344 15.704098 14.848108 +57 0 2.926405 9.143806 2.651302 +58 0 14.896721 7.858686 7.475072 +59 0 4.740279 12.830494 17.430934 +60 0 11.264234 17.880042 1.965988 +61 0 2.122788 2.710309 15.434044 +62 0 16.221404 13.542043 1.023542 +63 0 5.076289 17.860136 2.920203 +64 0 14.265919 0.729259 4.578851 +65 0 2.650163 18.039854 11.871156 +66 0 9.907093 16.824103 8.767583 +67 0 3.839564 6.575333 4.697998 +68 0 15.123267 2.383593 17.501794 +69 0 6.540603 1.383776 0.774982 +70 0 7.945906 2.605909 17.368903 +71 0 8.704276 15.208448 11.735172 +72 0 13.237416 6.037153 14.348603 +73 0 8.067571 13.364539 9.052999 +74 0 9.407962 4.902222 8.782698 +75 0 5.772582 0.873088 4.984489 +76 0 13.933641 12.144969 0.404453 +77 0 3.031529 0.563432 1.717590 +78 0 9.844876 2.668646 4.558840 +79 0 10.636467 6.884342 14.386562 +80 0 12.284218 15.941266 7.760652 +81 0 5.042671 11.213153 6.951564 +82 0 12.354308 18.213033 6.267982 +83 0 10.353297 5.136726 0.336169 +84 0 1.095563 6.000590 13.719188 +85 0 5.465277 2.156441 12.294467 +86 0 8.543844 4.470771 6.384907 +87 0 10.110532 0.718504 7.405707 +88 0 14.237080 11.715828 8.187193 +89 0 14.302341 6.192016 9.501457 +90 0 18.152972 7.763968 3.883909 +91 0 4.913776 14.036809 1.633707 +92 0 17.460944 12.697542 6.512363 +93 0 13.382369 5.456203 0.928643 +94 0 5.309432 2.871368 2.828555 +95 0 17.267186 12.687539 15.300565 +96 0 10.109989 13.353016 13.586974 +97 0 16.038267 16.406355 16.942367 +98 0 11.503743 12.891076 11.275134 +99 0 15.658094 10.986539 10.626163 +100 0 9.169738 1.032564 13.494495 +101 0 9.787192 11.446028 16.827203 +102 0 7.158441 9.971453 4.092223 +103 0 4.391326 8.291829 12.623212 +104 0 12.512983 3.741952 13.092402 +105 0 0.768056 15.770081 13.467752 +106 0 3.194780 10.954573 4.481072 +107 0 5.388984 5.082735 8.622369 +108 0 12.431148 13.544167 4.301546 +109 0 13.555206 14.716509 11.674598 +110 0 15.027329 6.443877 4.760399 +111 0 3.500374 15.396321 12.758939 +112 0 4.612389 6.659259 16.033432 +113 0 16.439294 7.953279 16.634083 +114 0 10.440887 1.264977 17.471020 +115 0 4.749051 18.421989 17.739409 +116 0 5.877249 8.664918 10.404692 +117 0 12.587218 8.751363 9.637651 +118 0 11.533788 5.194581 2.840659 +119 0 2.684053 1.912671 12.874147 +120 0 0.284052 13.184352 12.459776 +121 0 7.279246 6.069434 10.353867 +122 0 17.553987 9.468163 0.089587 +123 0 3.483024 0.371897 6.643496 +124 0 16.145377 4.400753 3.667256 +125 0 10.287752 7.265168 9.607225 +126 0 9.955883 15.813102 17.349136 +127 0 18.274221 15.358577 15.983473 +128 0 3.548562 8.654878 17.627983 +129 0 14.823749 3.176912 1.442758 +130 0 12.962944 8.015064 18.556139 +131 0 10.717552 13.597043 8.338394 +132 0 3.445497 7.906926 9.423231 +133 0 3.139143 5.007573 9.927598 +134 0 4.693100 4.588429 17.968608 +135 0 11.700165 3.765397 16.978834 +136 0 11.457212 1.985464 14.704452 +137 0 0.111632 12.665821 2.076924 +138 0 0.562804 17.428194 9.555229 +139 0 4.901644 15.643226 8.863999 +140 0 9.359318 7.685757 12.096960 +141 0 0.250709 5.411755 11.172989 +142 0 1.958458 6.272054 17.767389 +143 0 13.938619 9.131797 16.256382 +144 0 8.153892 5.831628 3.582313 +145 0 16.124144 5.918612 11.544635 +146 0 2.316068 15.099712 17.251637 +147 0 7.473063 4.337632 12.444118 +148 0 9.135377 17.017792 14.878537 +149 0 4.288046 5.417217 1.909319 +150 0 1.119915 11.364980 14.818019 +151 0 12.354102 10.355005 11.757563 +152 0 13.587739 8.102924 3.034136 +153 0 17.757244 16.820504 11.721001 +154 0 12.529316 17.070693 10.707541 +155 0 1.142484 12.099466 9.950078 +156 0 7.613522 16.733756 18.027140 +157 0 9.135876 0.772822 1.185189 +158 0 17.661879 2.094787 4.468992 +159 0 14.108794 15.533504 5.068347 +160 0 1.621115 17.793848 18.401390 +161 0 12.970668 9.407986 6.043816 +162 0 7.395746 12.874635 14.372563 +163 0 6.758971 16.006827 1.795054 +164 0 16.193377 17.688805 13.960053 +165 0 18.408477 1.210837 9.941091 +166 0 2.019800 2.711904 6.927264 +167 0 11.980019 15.570558 0.581226 +168 0 8.451391 10.300701 14.110722 +169 0 9.471675 9.384742 2.727582 +170 0 14.918974 16.113159 1.011162 +171 0 3.445730 13.048668 15.033230 +172 0 15.917696 13.047014 12.654031 +173 0 11.278518 10.951588 7.653872 +174 0 9.962884 2.426868 9.496351 +175 0 6.284059 14.703973 4.603315 +176 0 17.647046 3.889756 14.010681 +177 0 2.458519 13.272492 2.966876 +178 0 1.312273 10.362498 17.257626 +179 0 6.896579 1.830336 14.615491 +180 0 1.083357 3.547483 17.889213 +181 0 13.841506 8.698988 13.624772 +182 0 0.553593 1.674111 2.068709 +183 0 11.650904 12.915045 1.589931 +184 0 6.608270 8.158661 14.329472 +185 0 15.037612 18.216639 10.826783 +186 0 7.289548 5.596535 17.398567 +187 0 14.578809 11.971332 16.110505 +188 0 3.064919 17.157286 15.637841 +189 0 16.063019 8.658127 12.261281 +190 0 12.627360 3.194084 4.621713 +191 0 6.135715 6.806560 6.369703 +192 0 17.483994 3.167006 16.511470 +193 0 17.423139 9.375614 14.578500 +194 0 8.740352 13.559547 1.057657 +195 0 6.593292 17.705892 8.770206 +196 0 14.484462 18.375581 17.938524 +197 0 9.021835 9.465173 8.855075 +198 0 11.075214 9.792055 0.403522 +199 0 18.359278 15.205571 8.463916 +200 0 1.775548 12.673717 18.539494 +201 0 1.442422 11.993233 6.514585 +202 0 6.838328 14.743109 16.322220 +203 0 18.107358 1.589166 12.622319 +204 0 4.179444 3.953574 5.335255 +205 0 16.541209 14.676171 10.525495 +206 0 3.755501 5.611088 12.830949 +207 0 8.230846 16.138017 6.442526 +208 0 14.170509 2.315962 11.369409 +209 0 10.135232 18.493236 11.034458 +210 0 8.073981 12.710901 3.605555 +211 0 6.202286 15.795170 12.847552 +212 0 13.665773 0.565595 1.999473 +213 0 12.795908 4.807702 6.925677 +214 0 15.948468 1.848787 9.333664 +215 0 0.414508 10.175620 3.222119 +216 0 8.679693 16.825322 3.405716 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/grompp_cg.mdp new/csg-1.6.1/src/tools/references/spce/grompp_cg.mdp --- old/csg-1.6/src/tools/references/spce/grompp_cg.mdp 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/grompp_cg.mdp 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,15 @@ +title = CG Water +integrator = sd +tinit = 0 +dt = 0.002 +nsteps = 1 +nstxout = 1 +nstfout = 1 +nstlist = 1 +nstxout-compressed = 1 +coulombtype = Reaction-Field +rcoulomb = 0.9 +rvdw = 0.9 +tc-grps = System +tau_t = 0.5 +ref_t = 300 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/settings_re.xml new/csg-1.6.1/src/tools/references/spce/settings_re.xml --- old/csg-1.6/src/tools/references/spce/settings_re.xml 2020-04-18 05:01:25.000000000 +0200 +++ new/csg-1.6.1/src/tools/references/spce/settings_re.xml 2020-06-21 15:20:18.000000000 +0200 @@ -15,5 +15,11 @@ </cbspl> </re> </non-bonded> + <inverse> + <!-- System T = 300*0.00831451 kBT units --> + <kBT>2.4942</kBT> + <!-- scaling parameter for the update--> + <scale>0.5</scale> + </inverse> </cg> diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/topol_cg.top new/csg-1.6.1/src/tools/references/spce/topol_cg.top --- old/csg-1.6/src/tools/references/spce/topol_cg.top 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/topol_cg.top 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,21 @@ +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ + 1 1 no 1.0 1.0 + +[ atomtypes ] +;name at.num mass charge ptype c6 c12 + CG 8 18.01540 0.000 A 0.00000E+00 1.00000E+00 + +[ moleculetype ] +; molname nrexcl +SOL 1 + +[ atoms ] +; id at type res nr residu name at name +1 CG 1 SOL CG 1 0.000 + +[ system ] +CG water + +[ molecules ] +SOL 216 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.6/src/tools/references/spce/topol_cg.xml new/csg-1.6.1/src/tools/references/spce/topol_cg.xml --- old/csg-1.6/src/tools/references/spce/topol_cg.xml 1970-01-01 01:00:00.000000000 +0100 +++ new/csg-1.6.1/src/tools/references/spce/topol_cg.xml 2020-06-21 15:20:18.000000000 +0200 @@ -0,0 +1,8 @@ +<topology> + <molecules> + <molecule name="SOL" nmols="216" nbeads="1"> + <bead name="CG" type="CG" mass="18.0154" q="0" /> + </molecule> + </molecules> +</topology> + ++++++ votca-csg-manual-1.6.pdf -> votca-csg-manual-1.6.1.pdf ++++++ (binary differes) ++++++ votca-csg-tutorials-1.6.tar.gz -> votca-csg-tutorials-1.6.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-tutorials-1.6/.gitlab-ci.yml new/csg-tutorials-1.6.1/.gitlab-ci.yml --- old/csg-tutorials-1.6/.gitlab-ci.yml 2020-04-18 05:01:28.000000000 +0200 +++ new/csg-tutorials-1.6.1/.gitlab-ci.yml 2020-06-21 15:20:22.000000000 +0200 @@ -37,7 +37,7 @@ - pushd build - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DENABLE_WERROR=ON -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_REGRESSION_TESTING=${REGRESSION_TESTING:-ON} - -DBUILD_OWN_GROMACS=${BUILD_GROMACS} ${BUILD_GROMACS:+-DENABLE_WARNING_FLAGS=OFF} + -DBUILD_OWN_GROMACS=${BUILD_GROMACS} ${BUILD_GROMACS:+-DENABLE_WARNING_FLAGS=OFF -DENABLE_WERROR=OFF} -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install} - cmake --build . -- -j2 - ctest --output-on-failure @@ -88,38 +88,6 @@ CMAKE_BUILD_TYPE: "Release" extends: .build -Debug GCC Ubuntu: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Debug" - DISTRO: "ubuntu" - extends: .build - -Debug Clang Ubuntu: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Debug" - DISTRO: "ubuntu" - extends: .build - -Release GCC Ubuntu: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "ubuntu" - extends: .build - -Release Clang Ubuntu: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "ubuntu" - extends: .build - Release GCC Module: variables: CC: "gcc" @@ -128,70 +96,6 @@ MODULE_BUILD: "yes" extends: .build -Release GCC GMX2016: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016" - extends: .build - -Release Clang GMX2016: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016" - extends: .build - -Release GCC GMX2016D: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016_d" - extends: .build - -Release Clang GMX2016D: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2016_d" - extends: .build - -Release GCC GMX2018: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018" - extends: .build - -Release Clang GMX2018: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018" - extends: .build - -Release GCC GMX2018D: - variables: - CC: "gcc" - CXX: "g++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018_d" - extends: .build - -Release Clang GMX2018D: - variables: - CC: "clang" - CXX: "clang++" - CMAKE_BUILD_TYPE: "Release" - DISTRO: "fedora_gmx2018_d" - extends: .build - Release GCC GMX2019: variables: CC: "gcc" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-tutorials-1.6/CMakeLists.txt new/csg-tutorials-1.6.1/CMakeLists.txt --- old/csg-tutorials-1.6/CMakeLists.txt 2020-04-18 05:01:28.000000000 +0200 +++ new/csg-tutorials-1.6.1/CMakeLists.txt 2020-06-21 15:20:22.000000000 +0200 @@ -2,7 +2,7 @@ project(csg-tutorials) -set(PROJECT_VERSION "1.6") +set(PROJECT_VERSION "1.6.1") # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-tutorials-1.6/guide/README.md new/csg-tutorials-1.6.1/guide/README.md --- old/csg-tutorials-1.6/guide/README.md 2020-04-18 05:01:28.000000000 +0200 +++ new/csg-tutorials-1.6.1/guide/README.md 2020-06-21 15:20:22.000000000 +0200 @@ -22,8 +22,6 @@ make install ``` -The following option might be needed to disable sqlite3 libraries `-DWITH_SQLITE3=OFF`. - To build a gromacs version for VOTCA use ```bash
