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Merge branch 'master' into use-clang-format-demo

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# Conflicts:
#	unittest/force-styles/pair_style.cpp
#	unittest/utils/test_utils.cpp
This commit is contained in:
Axel Kohlmeyer
2020-06-15 16:14:13 -04:00
parent 65ff6bb617 4a3d9afb54
commit 14c22a004a
469 changed files with 790662 additions and 7532 deletions
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34
cmake/Modules/CodingStandard.cmake Normal file
View File

@ -0,0 +1,34 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python3_VERSION ${PYTHON_VERSION_STRING})
endif()
else()
find_package(Python3 COMPONENTS Interpreter QUIET)
endif()
if (Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for permission errors")
add_custom_target(
fix-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permission.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()
endif()

37
cmake/Modules/Documentation.cmake
View File

@ -2,10 +2,19 @@
# Build documentation
###############################################################################
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
endif()
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
@ -25,11 +34,10 @@ if(BUILD_DOC)
)
# download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${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)
@ -37,11 +45,18 @@ if(BUILD_DOC)
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 ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
"${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
endif()
# note, this may run in parallel with other tasks, so we must not use multiple processes here
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
)
# copy selected image files to html output tree
@ -56,17 +71,17 @@ if(BUILD_DOC)
set(HTML_IMAGE_TARGETS "")
foreach(_IMG ${HTML_EXTRA_IMAGES})
string(PREPEND _IMG JPG/)
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
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} html/JPG
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()
add_custom_target(
doc ALL
DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
)

12
cmake/Modules/LAMMPSUtils.cmake
View File

@ -96,9 +96,15 @@ function(FetchPotentials pkgfolder potfolder)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${LAMMPS_POTENTIALS_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach()
endif()
endfunction(FetchPotentials)

29
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -14,6 +14,29 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own")
# create variables to pass our compiler flags along to the subsystem compile
# need to apply -fallow-argument-mismatch, if the fortran compiler supports it
include(CheckFortranCompilerFlag)
check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
endif()
if(CMAKE_Fortran_FLAGS)
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
else()
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
endif()
if(CMAKE_CXX_FLAGS)
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
else()
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
if(CMAKE_C_FLAGS)
set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
else()
set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
@ -22,9 +45,9 @@ if(DOWNLOAD_SCAFACOS)
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw --with-internal-pfft
--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
F77=
BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a