Commit ce2b128c authored by Jacob Gissinger's avatar Jacob Gissinger
Browse files

Merge branch 'lammps-master' into bond/react-RMSD_constraint

parents bc49e854 583a09c8

.gitattributes

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+3 −0
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.gitattributes export-ignore

.gitignore export-ignore

.github export-ignore

.github/codecov.yml

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+29 −0
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comment: false

coverage:

  notify:

    slack:

      default:

        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="

        threshold: 10%

        only_pulls: false

        branches:

          - "master"

        flags:

          - "unit"

        paths:

          - "src"

  status:

    project:

        default:

            branches:

              - "master"

            paths:

              - "src"

            informational: true

    patch:

        default:

            branches:

              - "master"

            paths:

              - "src"

            informational: true

cmake/CMakeLists.txt

+9 −11
Original line number Diff line number Diff line
@@ -69,18 +69,10 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") 
  endif()

endif()



if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")

  set(CMAKE_TUNE_DEFAULT "-march=native")

endif()



if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")

  set(CMAKE_TUNE_DEFAULT "-march=native")

endif()



# we require C++11 without extensions

set(CMAKE_CXX_STANDARD 11)

set(CMAKE_CXX_STANDARD_REQUIRED ON)

set(CMAKE_CXX_EXTENSIONS OFF)

set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")



########################################################################

# User input options                                                   #
@@ -193,7 +185,7 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0") 
  target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})

endif()



option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)

option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})

if(LAMMPS_EXCEPTIONS)

  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)

endif()
@@ -366,7 +358,7 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD 
  endif()

endforeach()



set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")

set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")

separate_arguments(CMAKE_TUNE_FLAGS)

foreach(_FLAG ${CMAKE_TUNE_FLAGS})

  target_compile_options(lammps PRIVATE ${_FLAG})
@@ -755,6 +747,12 @@ if (${_index} GREATER -1) 
endif()

message(STATUS "<<< Linker flags: >>>")

message(STATUS "Executable name:  ${LAMMPS_BINARY}")

if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)

  get_target_property(OPTIONS lammps LINK_OPTIONS)

  if(OPTIONS)

    message(STATUS "Linker options:   ${OPTIONS}")

  endif()

endif()

if(CMAKE_EXE_LINKER_FLAGS)

  message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")

endif()

cmake/Modules/Documentation.cmake

+54 −36
Original line number Diff line number Diff line
@@ -15,75 +15,93 @@ if(BUILD_DOC) 
    endif()

    set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})

  endif()

  find_package(Doxygen 1.8.10 REQUIRED)



  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)





  add_custom_command(

    OUTPUT docenv

    COMMAND ${VIRTUALENV} docenv

  )



  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)

  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)



  set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)

  set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)

  set(SPHINX_STATIC_DIR  ${SPHINX_CONFIG_DIR}/_static)



  # configuration and static files are copied to binary dir to avoid collisions with parallel builds

  set(DOC_BUILD_DIR ${CMAKE_CURRENT_BINARY_DIR}/doc)

  set(DOC_BUILD_CONFIG_FILE ${DOC_BUILD_DIR}/conf.py)

  set(DOC_BUILD_STATIC_DIR ${DOC_BUILD_DIR}/_static)

  set(DOXYGEN_BUILD_DIR ${DOC_BUILD_DIR}/doxygen)

  set(DOXYGEN_XML_DIR ${DOXYGEN_BUILD_DIR}/xml)



  # copy entire configuration folder to doc build directory

  # files in _static are automatically copied during sphinx-build, so no need to copy them individually

  file(COPY ${SPHINX_CONFIG_DIR}/ DESTINATION ${DOC_BUILD_DIR})



  # configure paths in conf.py, since relative paths change when file is copied

  configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})



  add_custom_command(

    OUTPUT requirements.txt

    DEPENDS docenv

    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt

    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade

    OUTPUT ${DOC_BUILD_DIR}/requirements.txt

    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}

    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt

    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip

    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters

    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade

  )



  # download mathjax distribution and unpack to folder "mathjax"

  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)

  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)

    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"

      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"

      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)

    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

    file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)

    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)

    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

  endif()

  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)

  file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)



  # for increased browser compatibility

  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)

  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)

    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"

      "${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")

      "${DOC_BUILD_STATIC_DIR}/polyfill.js")

  endif()



  # note, this may run in parallel with other tasks, so we must not use multiple processes here

  # set up doxygen and add targets to run it

  file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})

  file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)

  configure_file(${LAMMPS_DOC_DIR}/doxygen/Doxyfile.in ${DOXYGEN_BUILD_DIR}/Doxyfile)

  get_target_property(LAMMPS_SOURCES lammps SOURCES)

  add_custom_command(

    OUTPUT html

    DEPENDS ${DOC_SOURCES} docenv requirements.txt

    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html

    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html

    OUTPUT ${DOXYGEN_XML_DIR}/index.xml

    DEPENDS ${DOC_SOURCES} ${LAMMPS_SOURCES}

    COMMAND Doxygen::doxygen ${DOXYGEN_BUILD_DIR}/Doxyfile WORKING_DIRECTORY ${DOXYGEN_BUILD_DIR}

    COMMAND ${CMAKE_COMMAND} -E touch ${DOXYGEN_XML_DIR}/run.stamp

  )



  # copy selected image files to html output tree

  file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/JPG)

  set(HTML_EXTRA_IMAGES balance_nonuniform.jpg balance_rcb.jpg

    balance_uniform.jpg bow_tutorial_01.png bow_tutorial_02.png

    bow_tutorial_03.png bow_tutorial_04.png bow_tutorial_05.png

    dump1.jpg dump2.jpg examples_mdpd.gif gran_funnel.png gran_mixer.png

    hop1.jpg hop2.jpg saed_ewald_intersect.jpg saed_mesh.jpg

    screenshot_atomeye.jpg screenshot_gl.jpg screenshot_pymol.jpg

    screenshot_vmd.jpg sinusoid.jpg xrd_mesh.jpg)

  set(HTML_IMAGE_TARGETS "")

  foreach(_IMG ${HTML_EXTRA_IMAGES})

    string(PREPEND _IMG JPG/)

    list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")

  if(EXISTS ${DOXYGEN_XML_DIR}/run.stamp)

    set(SPHINX_EXTRA_OPTS "-E")

  else()

    set(SPHINX_EXTRA_OPTS "")

  endif()

  add_custom_command(

      OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}

      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG

      COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}

    OUTPUT html

    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}

    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html

    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html

    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF

    COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

  )

  endforeach()



  add_custom_target(

    doc ALL

    DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}

    DEPENDS html ${DOC_BUILD_STATIC_DIR}/mathjax/es5

    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}

  )



  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})

  install(DIRECTORY ${DOC_BUILD_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})

endif()

cmake/Modules/GTest.cmake

+8 −6
Original line number Diff line number Diff line
@@ -7,9 +7,11 @@ else() 
endif()



include(ExternalProject)

set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")

mark_as_advanced(GTEST_URL)

ExternalProject_Add(googletest

                    GIT_REPOSITORY  https://github.com/google/googletest.git

                    GIT_TAG         release-1.10.0

                    URL ${GTEST_URL}

                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd

                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"

                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"

                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
@@ -52,26 +54,26 @@ add_library(GTest::GTest UNKNOWN IMPORTED) 
set_target_properties(GTest::GTest PROPERTIES

        IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}

        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}

        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})

        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")

add_dependencies(GTest::GTest googletest)



add_library(GTest::GMock UNKNOWN IMPORTED)

set_target_properties(GTest::GMock PROPERTIES

        IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}

        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}

        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})

        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")

add_dependencies(GTest::GMock googletest)



add_library(GTest::GTestMain UNKNOWN IMPORTED)

set_target_properties(GTest::GTestMain PROPERTIES

        IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}

        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}

        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})

        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")

add_dependencies(GTest::GTestMain googletest)



add_library(GTest::GMockMain UNKNOWN IMPORTED)

set_target_properties(GTest::GMockMain PROPERTIES

        IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}

        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}

        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})

        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")

add_dependencies(GTest::GMockMain googletest)

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