Merge pull request #124 from votca/stable_bump

Merge 2021-dev into stable

Author: junghans

.gitattributes

@@ -0,0 +1,6 @@
+.gitattributes export-ignore
+.gitignore export-ignore
+.gitmodules export-ignore
+.github export-ignore
+.clang-format export-ignore
+.codecov.yml export-ignore

.github/workflows/continuous-integration-workflow.yml

@@ -10,7 +10,7 @@ jobs:
     continue-on-error: ${{ matrix.distro == 'ubuntu:devel' || matrix.distro == 'opensuse:latest' || matrix.distro == 'fedora:rawhide' || matrix.continue-on-error == true }}
     strategy:
       matrix:
-        distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest', 'ubuntu:18.04']
+        distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest']
         toolchain: [gnu]
         cmake_build_type: [Release]
         minimal: [false]
@@ -58,7 +58,7 @@ jobs:
           key: ${{ steps.setup.outputs.cache_key }}
           restore-keys: ${{ steps.setup.outputs.cache_restore_key }}
       - name: CMake
-        run: mkdir builddir && cd builddir && cmake ${{ steps.setup.outputs.cmake_args }} ../votca
+        run: cmake -B builddir ${{ steps.setup.outputs.cmake_args }} votca
       - name: Build
         run: |
           ccache -z

.github/workflows/copyright.yml

@@ -0,0 +1,40 @@
+name: Copyright
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  edit:
+    name: Copyright
+    if: ${{ github.event.comment.body == '@votca-bot copyright' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if message comes from PR
+        uses: octokit/[email protected]
+        id: issue_info
+        with:
+          route: GET /repos/:repository/issues/:pull_number
+          repository: ${{ github.repository }}
+          pull_number: ${{ github.event.issue.number }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Get PR info
+        if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
+        uses: octokit/[email protected]
+        id: pr_info
+        with:
+          route: GET /repos/:repository/pulls/:pull_number
+          repository: ${{ github.repository }}
+          pull_number: ${{ github.event.issue.number }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Checkout head branch from PR
+        if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
+        uses: actions/[email protected]
+        with:
+          repository: ${{ fromJSON(steps.pr_info.outputs.data).head.repo.full_name }}
+          ref: ${{ fromJSON(steps.pr_info.outputs.data).head.ref }}
+          fetch-depth: 0
+          token: ${{ secrets.VOTCA_BOT_TOKEN }}
+      - name: Create and commit copyright updates
+        if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
+        uses: votca/actions/copyright@master
+        with:
+          base: ${{ fromJSON(steps.pr_info.outputs.data).base.sha }}

CMakeLists.txt

@@ -1,31 +1,45 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.12)
 
-project(csg-tutorials)
+project(csg-tutorials LANGUAGES NONE)
 
-set(PROJECT_VERSION "1.6.4")
+set(PROJECT_VERSION "2021-dev")
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
 
+# not used, but stops GNUInstallDirs.cmake from warning
+set(CMAKE_INSTALL_LIBDIR "lib64")
 include(GNUInstallDirs)
+include(FeatureSummary)
 
 option(ENABLE_REGRESSION_TESTING "Build and copy regression testing stuff" OFF)
+add_feature_info(ENABLE_REGRESSION_TESTING ENABLE_REGRESSION_TESTING "Enable regression tests")
 if(ENABLE_REGRESSION_TESTING)
   option(ENABLE_EXPERIMENTAL_TESTS "Run more unstable regression tests as well" OFF)
+  add_feature_info(ENABLE_EXPERIMENTAL_TESTS ENABLE_EXPERIMENTAL_TESTS "Enable experimental regression tests")
+  enable_language(CXX) # needed by mpi for VOTCA_CSG
   enable_testing()
   find_package(LMP)
+  set_package_properties(LMP PROPERTIES TYPE OPTIONAL PURPOSE "Lammps binary needed to run lammps regression tests")
   find_package(MDRUN_MPI)
+  set_package_properties(MDRUN_MPI PROPERTIES TYPE OPTIONAL PURPOSE "gromacs mpi binary needed to run parallel gromacs regression tests")
   if(MDRUN_MPI_FOUND)
     find_package(MPI)
+    set_package_properties(MPI PROPERTIES TYPE OPTIONAL PURPOSE "mpiexec binary needed to run parallel gromacs regression tests")
     set(NPROCS 4 CACHE STRING "# processes for testing")
     if(DEFINED MPIEXEC_MAX_NUMPROCS AND NPROCS GREATER MPIEXEC_MAX_NUMPROCS)
        message(WARNING "NPROCS(${NPROCS}) bigger than MPIEXEC_MAX_NUMPROCS(${MPIEXEC_MAX_NUMPROCS}) appending '--oversubscribe'")
        set(MPIEXEC_PREFLAGS "${MPIEXEC_PREFLAGS} --oversubscribe")
     endif()
   endif()
   find_package(ESPRESSO)
+  set_package_properties(ESPRESSO PROPERTIES TYPE OPTIONAL PURPOSE "ESPResSo MD python module needed to run ESPResSo MD regression tests")
   find_package(CMA)
+  set_package_properties(CMA PROPERTIES TYPE OPTIONAL PURPOSE "CMA python module needed to run CMA regression tests")
+  find_package(Gnuplot)
+  set_package_properties(Gnuplot PROPERTIES TYPE OPTIONAL PURPOSE "gnuplot needed to run CMA/simplex regression tests")
   find_package(VOTCA_CSG NO_MODULE REQUIRED)
+  set_package_properties(VOTCA_CSG PROPERTIES TYPE REQUIRED PURPOSE "VOTCA csg binaries used in testing")
   if(DEFINED VOTCA_CSG_VERSION AND NOT VOTCA_CSG_VERSION STREQUAL PROJECT_VERSION)
     message(FATAL_ERROR "Incompatible VOTCA CSG version found (needed ${PROJECT_VERSION}, found ${VOTCA_CSG_VERSION})")
   endif()
@@ -58,6 +72,9 @@ if(ENABLE_REGRESSION_TESTING)
     if(NOT CMA_FOUND AND DIR MATCHES "cma/")
       continue()
     endif()
+    if(NOT Gnuplot_FOUND AND DIR MATCHES "(cma/|simplex|realtime)")
+      continue()
+    endif()
     if(NOT ENABLE_EXPERIMENTAL_TESTS)
       if(DIR MATCHES "some/broken/test")
         continue()
@@ -105,23 +122,41 @@ if(ENABLE_REGRESSION_TESTING)
   message(STATUS "Use VOTCASHARE=${VOTCA_SHARE} PATH=${VOTCA_PATH}:\$PATH VOTCA_CSG_DEFAULTS=${VOTCA_CSG_DEFAULTS} for out-of-cmake testing")
 endif()
 
+if(VOTCA_SPHINX_DIR)
+  file(GLOB RSTS ${CMAKE_CURRENT_SOURCE_DIR}/guide/*.rst)
+  set(MANUAL_RST_FILES)
+  foreach(_RST ${RSTS})
+    get_filename_component(_FILE "${_RST}" NAME)
+    add_custom_command(OUTPUT ${VOTCA_SPHINX_DIR}/csg-tutorials/${_FILE}
+      COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_RST} ${VOTCA_SPHINX_DIR}/csg-tutorials/${_FILE}
+      DEPENDS ${_RST})
+    list(APPEND MANUAL_RST_FILES ${VOTCA_SPHINX_DIR}/csg-tutorials/${_FILE})
+  endforeach()
+  add_custom_target(doc-csg-tutorials DEPENDS ${MANUAL_RST_FILES} ${MANUAL_PNG_FILES})
+endif()
+
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/ DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/csg-tutorials
 	PATTERN ".git*" EXCLUDE PATTERN "step_*" EXCLUDE
 	PATTERN "CMake*" EXCLUDE PATTERN "cmake_install.cmake" EXCLUDE
 	PATTERN "install_manifest.txt" EXCLUDE PATTERN "*~" EXCLUDE
 	PATTERN "inverse.log" EXCLUDE)
 
-configure_file(${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake IMMEDIATE @ONLY)
+configure_file(${PROJECT_SOURCE_DIR}/CMakeModules/cmake_uninstall.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake IMMEDIATE @ONLY)
 option(ENABLE_TESTING "Test if cmake worked" OFF)
+add_feature_info(ENABLE_TESTING ENABLE_TESTING "Enable unit tests")
 if(ENABLE_TESTING)
   enable_testing()
   add_test(regression_UninstallExists ${CMAKE_COMMAND} -DFileToCheck=${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
            -P ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FileExists.cmake)
 
-  set_tests_properties(regression_UninstallExists PROPERTIES LABELS "regression")
+  set_tests_properties(regression_UninstallExists PROPERTIES LABELS "csg-tutorials;votca")
 endif(ENABLE_TESTING)
 add_custom_target(uninstall-csg-tutorials COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
 if(NOT TARGET uninstall)
   add_custom_target(uninstall)
 endif()
 add_dependencies(uninstall uninstall-csg-tutorials)
+
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+  feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
+endif (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)

README

@@ -0,0 +1,132 @@
+|Codacy Badge| |codecov| |CI| |DOI|
+
+This is a collection of coarse-graining tutorials using the VOTCA
+package. Further information on VOTCA can be found at
+http://www.votca.org
+
+The development of VOTCA is mainly funded by academic research grants.
+If you use this package, please cite the VOTCA papers:
+
+-  | *Relative entropy and optimization-driven coarse-graining methods
+     in VOTCA*,
+   | S.Y. Mashayak, M. Jochum, K. Koschke, N.R. Aluru, V. Ruehle, and C.
+     Junghans,
+   | `PLoS one 10, e131754
+     (2015) <http://dx.doi.org/10.1371/journal.pone.0131754>`__.
+
+-  | *Hybrid approaches to coarse-graining using the VOTCA package:
+     liquid hexane*,
+   | V. Ruehle and C. Junghans,
+   | `Macromol. Theory Simul. 20, 472
+     (2011) <http://dx.doi.org/10.1002/mats.201100011>`__.
+
+-  | *Versatile Object-oriented Toolkit for Coarse-graining
+     Applications*,
+   | V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, and D. Andrienko,
+   | `J. Chem. Theo. Comp. 5 (12), 3211
+     (2009) <http://dx.doi.org/10.1021/ct900369w>`__.
+
+In case of questions, please post them in the google discussion group
+for votca at http://groups.google.com/group/votca
+
+You can contact the VOTCA Development Team at [email protected].
+
+The following tutorials (compare with paper above) are included. They
+all rely on Gromacs unless specified otherwise:
+
+-  ``spce/atomistic``: atomistic reference simulations for SPC/E water
+-  ``spce/force_matching``: force matching for SPC/E water
+-  ``spce/ibi``: iterative boltzmann inversion for SPC/E water
+-  ``spce/ibi_pressure``: iterative boltzmann inversion for SPC/E water
+   with simple pressure correction
+-  ``spce/ibi_pressure_wjk``: iterative boltzmann inversion for SPC/E
+   water with wjk pressure correction
+-  ``spce/ibi_hoomd-blue``: iterative boltzmann inversion for SPC/E
+   water using hoomd-blue
+-  ``spce/ibi_dlpoly``: iterative boltzmann inversion for SPC/E water
+   using dl\_poly
+-  ``spce/ibi_espresso``: iterative boltzmann inversion for SPC/E water
+   using ESPResSo
+-  ``spce/ibi_espressopp``: iterative boltzmann inversion for SPC/E
+   water using ESPResSo++
+-  ``spce/ibi_lammps``: iterative boltzmann inversion for SPC/E water
+   using LAMMPS
+-  ``spce/ibi_gromacs-multi``: iterative boltzmann inversion for SPC/E
+   water using GROMACS' multidir feature
+-  ``spce/imc`` inverse monte carlo for SPC/E water
+-  ``spce/re``: relative entropy method for SPC/E water
+-  ``spce/re_lammps``: relative entropy method for SPC/E water using
+   LAMMPS
+-  ``spce/realtime``: iterative boltzmann inversion realtime tutorial
+   for SPC/E water
+-  ``spce/realtime_lammps``: iterative boltzmann inversion realtime
+   tutorial for SPC/E water using LAMMPS
+-  ``spce/simplex``: simplex optimization for SPC/E water
+
+   -  ``spce/simplex/simple``: optimizing the rdf
+   -  ``spce/simplex/pressure``: optimizing the rdf and pressure
+   -  ``spce/simplex/density``: optimizing the rdf and density
+
+-  ``spce/cma``: cma optimization for SPC/E water
+
+   -  ``spce/cma/simple``: optimizing the rdf
+   -  ``spce/cma/density``: optimizing the rdf and the density
+
+-  ``methanol/atomistic``: atomistic simulations for methanol
+-  ``methanol/force_matching``: force matching for methanol
+-  ``methanol/ibi``: iterative boltzmann inversion for methanol
+-  ``methanol/imc``: inverse monte carlo for methanol
+-  ``methanol/imc_gromacs-remd``: inverse monte carlo for methanol with
+   REMD (only for gromacs) during iterations
+
+-  ``propane/atomistic``: atomistic simulations for liquid propane
+-  ``propane/ibi``: iterative boltzmann inversion for nonbonded
+   interactions of liquid propane
+-  ``propane/imc``: inverse monte carlo for nonbonded interactions of
+   liquid propane
+-  ``propane/single_chain``: atomistic simulations, boltzmann inversion
+   and force matching for a single chain of propane
+
+-  ``hexane/atomistic``: atomistic simulations for liquid hexane
+-  ``hexane/force_matching``: force matching (bonded and nonbonded
+   interactions of liquid hexane
+-  ``hexane/ibi_all``: iterative boltzmann inversion for bonded and
+   nonbonded interactions of liquid hexane
+-  ``hexane/ibi_nonbonded``: iterative boltzmann inversion for only
+   nonbonded interactions of liquid hexane
+-  ``hexane/hybrid_force_matching``: hybrid force matching of only
+   nonbonded interactions (with bonded interactions from boltzmann
+   inversion)
+
+-  ``methanol-water``: methanol-water mixture for 3 different
+   concentrations
+
+   -  \`methanol-water/\*/atomistic atomistic simulations
+   -  ``methanol-water/*/re``: relative entropy method
+   -  ``methanol-water/*/simplex``: simplex optimizing
+
+-  ``urea-water/atomistic``: atomistic reference simulations urea-water
+   mixture
+-  ``urea-water/kb-ibi``: Kirkwood-Buff coarse-graining (see Ganguly et
+   al. J. Chem. Theo. Comp., 8, 1802 (2012) for details)
+-  ``urea-water/cibi``: Coordination iterative Boltzmann inversion (see
+   T. E. de Oliveira et al., JCP 144, 174106 (2016) for details) -
+   different molarity than kb-ibi
+-  ``urea-water/cibi/pre``: IBI preparation run for cibi
+-  ``urea-water/ibi``: boltzmann inversion (to compare to kb-ibi)
+
+-  ``LJ1-LJ2/imc``: regularization of inverse Monte-Carlo (see
+   Rosenberger et al. Eur. Phys. J. Special Topics 225, 1323-1345 (2016)
+   for details)
+
+Each of the tutorials contains a ``run.sh`` which lists all commands
+needed to execute the tutorial.
+
+.. |Codacy Badge| image:: https://app.codacy.com/project/badge/Grade/677ff88de55e46ee9411e2eaa6248e0c
+   :target: https://www.codacy.com/gh/votca/csg-tutorials?utm_source=github.com&utm_medium=referral&utm_content=votca/csg-tutorials&utm_campaign=Badge_Grade
+.. |codecov| image:: https://codecov.io/gh/votca/csg-tutorials/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/votca/csg-tutorials
+.. |CI| image:: https://github.com/votca/votca/workflows/CI/badge.svg?branch=master
+   :target: https://github.com/votca/votca/actions?query=workflow%3ACI+branch%3Amaster
+.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3902713.svg
+   :target: https://doi.org/10.5281/zenodo.3902713