Merge remote-tracking branch 'origin/master' into zstd_support

2020-09-01 12:58:41 -04:00
parent 40ea03234f 24f5807623
commit 31bd76efa5
2104 changed files with 34692 additions and 82065 deletions
--- a/cmake/Modules/Documentation.cmake
+++ b/cmake/Modules/Documentation.cmake
@ -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
+    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 requirements.txt --upgrade
+    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}")
-    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}
-    )
-  endforeach()
+  if(EXISTS ${DOXYGEN_XML_DIR}/run.stamp)
+    set(SPHINX_EXTRA_OPTS "-E")
+  else()
+    set(SPHINX_EXTRA_OPTS "")
+  endif()
+  add_custom_command(
+    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
+  )

  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 ${CMAKE_INSTALL_DOCDIR})
 endif()
--- a/cmake/Modules/Packages/GPU.cmake
+++ b/cmake/Modules/Packages/GPU.cmake
@ -75,7 +75,7 @@ if(GPU_API STREQUAL "CUDA")
  endif()
  # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
  endif()
  # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
  if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
  include(ExternalProject)
  ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
-    URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
+    URL https://github.com/kokkos/kokkos/archive/3.2.00.tar.gz
+    URL_MD5 81569170fe232e5e64ab074f7cca5e50
    CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
  )
@ -50,7 +50,7 @@ if(DOWNLOAD_KOKKOS)
  target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
  add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.1.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.2.00 REQUIRED CONFIG)
  target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)