Unverified Commit 01f97f19 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into restrain_lbound

parents 0796a703 80311891

.gitignore

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@@ -9,6 +9,7 @@ 
*.d

*.d

*.x

*.x

*.exe

*.exe

*.sif

*.dll

*.dll

*.pyc

*.pyc

__pycache__

__pycache__

cmake/CMakeLists.txt

+240 −259

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cmake/FindLAMMPS.cmake.in

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# - Find liblammps

# Find the native liblammps headers and libraries.

#

# The following variables will set:

#  LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.

#  LAMMPS_LIBRARIES    - List of libraries when using lammps.

#  LAMMPS_API_DEFINES  - lammps library api defines

#  LAMMPS_VERSION      - lammps library version 

#  LAMMPS_FOUND        - True if liblammps found.

#

# In addition a LAMMPS::LAMMPS imported target is getting created.

#

#  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

#  http://lammps.sandia.gov, Sandia National Laboratories

#  Steve Plimpton, sjplimp@sandia.gov

#

#  Copyright (2003) Sandia Corporation.  Under the terms of Contract

#  DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

#  certain rights in this software.  This software is distributed under

#  the GNU General Public License.

#

#  See the README file in the top-level LAMMPS directory.

#



find_package(PkgConfig)



pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)

find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)



set(LAMMPS_VERSION @LAMMPS_VERSION@)

set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)



find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)



set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")

set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")



include(FindPackageHandleStandardArgs)

# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE

# if all listed variables are TRUE

find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)



mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)



if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)

  add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)

  set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")

endif()

cmake/LAMMPSConfig.cmake.in

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set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})

include(CMakeFindDependencyMacro)

if(@BUILD_MPI@)

  find_dependency(MPI REQUIRED CXX)

endif()

if(@PKG_KSPACE@)

  if(@FFT@ STREQUAL "FFTW3")

    find_dependency(@FFTW@ REQUIRED MODULE)

  endif()

endif()

if(NOT @BUILD_SHARED_LIBS@)

  if(@BUILD_OMP@)

    find_dependency(OpenMP REQUIRED)

  endif()

  if(@WITH_JPEG@)

    find_dependency(JPEG REQUIRED)

  endif()

  if(@WITH_PNG@)

    find_dependency(PNG REQUIRED)

    find_dependency(ZLIB REQUIRED)

  endif()

  if(@PKG_KIM@)

    find_dependency(PkgConfig REQUIRED)

    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)

    if(@CURL_FOUND@)

      find_dependency(CURL REQUIRED)

    endif()

  endif()

  if(@PKG_USER-SMD@)

    find_dependency(Eigen3 NO_MODULE REQUIRED)

  endif()

  if(@PKG_USER-SCAFACOS@)

    find_dependency(PkgConfig REQUIRED)

    find_ependency(GSL REQUIRED)

    find_dependency(MPI REQUIRED C Fortran)

    pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)

  endif()

  if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)

    find_package(Python REQUIRED COMPONENTS Development)

  endif()

  if(@PKG_COMPRESS@)

    find_dependency(ZLIB REQUIRED)

  endif()

  if(@PKG_KOKKOS@)

    if(@EXTERNAL_KOKKOS@)

      find_dependency(Kokkos 3 REQUIRED)

    endif()

  endif()

  if(@PKG_VORONOI@)

    find_dependency(VORO REQUIRED)

  endif()

  if(@PKG_USER-INTEL@)

    if(@INTEL_LRT_MODE@ STREQUAL "THREADS")

      find_dependency(Threads REQUIRED)

    endif()

    if(@TBB_MALLOC_FOUND@)

      find_ependency(TBB_MALLOC REQUIRED)

    endif()

  endif()

  if(@PKG_USER-ADIOS@)

    find_ependency(ADIOS2 REQUIRED)

  endif()

  if(@PKG_LATTE@)

    find_ependency(LATTE REQUIRED)

  endif()

  if(@PKG_MESSAGE@)

    if(@MESSAGE_ZMQ@)

      find_ependency(ZMQ REQUIRED)

    endif()

  endif()

  if(@PKG_MSCG@)

    find_ependency(GSL REQUIRED)

    find_ependency(MSCG REQUIRED)

  endif()

  if(@USER-NETCDF@)

    if(@NETCDF_FOUND@)

      find_ependency(NetCDF REQUIRED)

    endif()

    if(@PNETCDF_FOUND@)

      find_ependency(PNetCDF REQUIRED)

    endif()

  endif()

  if(@PKG_QUIP@)

    find_ependency(QUIP REQUIRED)

  endif()

endif()

include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/Documentation.cmake

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

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

# Build documentation

# Build documentation

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

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

option(BUILD_DOC "Build LAMMPS documentation" OFF)

option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)

if(BUILD_DOC)

if(BUILD_DOC)

  include(ProcessorCount)

  ProcessorCount(NPROCS)

  find_package(PythonInterp 3 REQUIRED)

  find_package(PythonInterp 3 REQUIRED)





  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)

  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
@@ -26,15 +24,49 @@ if(BUILD_DOC) 
    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters

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

  )

  )





  # 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)

    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)

  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/)



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

  add_custom_command(

  add_custom_command(

    OUTPUT html

    OUTPUT html

    DEPENDS ${DOC_SOURCES} docenv requirements.txt

    DEPENDS ${DOC_SOURCES} docenv requirements.txt

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

    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

  )



  # 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 "html/${_IMG}")

    add_custom_command(

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

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

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

    )

    )

  endforeach()





  add_custom_target(

  add_custom_target(

    doc ALL

    doc ALL

    DEPENDS html

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

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

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

  )

  )

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