Unverified Commit efd81a28 authored by Jacob Gissinger's avatar Jacob Gissinger Committed by GitHub
Browse files

Merge branch 'master' into bond/react-efficient-competing_reactions

parents a5f7b418 09ef2bc8

.gitignore

+2 −0
Original line number Diff line number Diff line 
*~

*.o

*.so

*.lo

*.cu_o

*.ptx

*_ptx.h
@@ -32,6 +33,7 @@ log.cite 
.Trashes

ehthumbs.db

Thumbs.db

.clang-format



#cmake

/build*

cmake/CMakeLists.txt

+128 −23
Original line number Diff line number Diff line
@@ -43,6 +43,29 @@ function(validate_option name values) 
    endif()

endfunction(validate_option)



function(get_lammps_version version_header variable)

    file(READ ${version_header} line)

    set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)

    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")

    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")

    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")

    string(STRIP ${day} day)

    string(STRIP ${month} month)

    string(STRIP ${year} year)

    list(FIND MONTHS "${month}" month)

    string(LENGTH ${day} day_length)

    string(LENGTH ${month} month_length)

    if(day_length EQUAL 1)

        set(day "0${day}")

    endif()

    if(month_length EQUAL 1)

        set(month "0${month}")

    endif()

    set(${variable} "${year}${month}${day}" PARENT_SCOPE)

endfunction()



get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)



# Cmake modules/macros are in a subdirectory to keep this file cleaner

set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
@@ -113,6 +136,7 @@ if(BUILD_EXE) 
  if(LAMMPS_MACHINE)

    set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")

  endif()

  set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})

endif()



option(BUILD_LIB "Build LAMMPS library" OFF)
@@ -121,10 +145,10 @@ if(BUILD_LIB) 
  if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg

    set(CMAKE_POSITION_INDEPENDENT_CODE ON)

  endif()

  set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")

  mark_as_advanced(LIB_SUFFIX)

  if(LIB_SUFFIX)

    set(LIB_SUFFIX "_${LIB_SUFFIX}")

  set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")

  mark_as_advanced(LAMMPS_LIB_SUFFIX)

  if(LAMMPS_LIB_SUFFIX)

    set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")

  endif()

endif()
@@ -183,12 +207,55 @@ endif() 
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)



option(ENABLE_TESTING "Enable testing" OFF)

if(ENABLE_TESTING)

if(ENABLE_TESTING AND BUILD_EXE)

  enable_testing()

endif(ENABLE_TESTING)

  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")

  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")

  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)



  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)

    include(FetchContent)



    FetchContent_Declare(lammps-testing

      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git

      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}

    )



    FetchContent_GetProperties(lammps-testing)

    if(NOT lammps-testing_POPULATED)

      message(STATUS "Downloading tests...")

      FetchContent_Populate(lammps-testing)

    endif()



    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})

  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)

    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"

                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")

  endif()



  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})

    message(STATUS "Running test discovery...")



    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)

    foreach(script_path ${TEST_SCRIPTS})

      get_filename_component(TEST_NAME ${script_path} EXT)

      get_filename_component(SCRIPT_NAME ${script_path} NAME)

      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)

      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)

      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})

      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})

      set(TEST_NAME "test_core_${TEST_NAME}_serial")

      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})

      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})

    endforeach()

    list(LENGTH TEST_SCRIPTS NUM_TESTS)



    message(STATUS "Found ${NUM_TESTS} tests.")

  endif()

endif()



set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP

  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP

  SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS

  USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE

  USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -412,8 +479,8 @@ endif() 


if(PKG_USER-NETCDF)

  find_package(NetCDF REQUIRED)

  include_directories(NETCDF_INCLUDE_DIR)

  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})

  include_directories(${NETCDF_INCLUDE_DIRS})

  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})

  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)

endif()
@@ -481,6 +548,39 @@ if(PKG_KIM) 
  include_directories(${KIM_INCLUDE_DIRS})

endif()



if(PKG_MESSAGE)

  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F

      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)



  if(BUILD_SHARED_LIBS)

      add_library(cslib SHARED ${cslib_SOURCES})

  else()

      add_library(cslib STATIC ${cslib_SOURCES})

  endif()



  if(BUILD_MPI)

    target_compile_definitions(cslib PRIVATE -DMPI_YES)

    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")

  else()

    target_compile_definitions(cslib PRIVATE -DMPI_NO)

    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")

  endif()



  if(MESSAGE_ZMQ)

    target_compile_definitions(cslib PRIVATE -DZMQ_YES)

    find_package(ZMQ REQUIRED)

    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})

    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})

  else()

    target_compile_definitions(cslib PRIVATE -DZMQ_NO)

    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)

  endif()



  list(APPEND LAMMPS_LINK_LIBS cslib)

  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)

endif()



if(PKG_MSCG)

  find_package(GSL REQUIRED)

  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
@@ -678,7 +778,9 @@ if(PKG_USER-OMP) 
    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp

                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp

                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp

                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)

                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp

                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)

    add_definitions(-DLMP_USER_OMP)

    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")



    # detects styles which have USER-OMP version
@@ -1011,7 +1113,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR}) 
######################################

set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")

set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")

foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})

set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})

list(SORT temp_PKG_LIST)

foreach(PKG ${temp_PKG_LIST})

    if(PKG_${PKG})

        set(temp "${temp}  \"${PKG}\",\n")

    endif()
@@ -1036,14 +1140,14 @@ if(BUILD_LIB) 
  if(LAMMPS_DEPS)

    add_dependencies(lammps ${LAMMPS_DEPS})

  endif()

  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})

  if(BUILD_SHARED_LIBS)

  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})

  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})

  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)

    configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)

    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)

  endif()

  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)

  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)

  configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)

  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)

else()

  list(APPEND LMP_SOURCES ${LIB_SOURCES})

endif()
@@ -1059,10 +1163,11 @@ if(BUILD_EXE) 
    endif()

  endif()

  

  set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})

  set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})

  install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})

  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)

  if(ENABLE_TESTING)

    add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)

    add_test(ShowHelp ${LAMMPS_BINARY} -help)

  endif()

endif()
@@ -1130,7 +1235,7 @@ endif() 
# Install potential files in data directory

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

set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)

install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)

install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})



configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)

configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
@@ -1172,7 +1277,7 @@ endif() 
###############################################################################

# Print package summary

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

foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})

foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})

  if(PKG_${PKG})

    message(STATUS "Building package: ${PKG}")

  endif()

cmake/FindLAMMPS.cmake.in

0 → 100644
+48 −0
Original line number Diff line number Diff line 
# - 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/Modules/FindZMQ.cmake

0 → 100644
+8 −0
Original line number Diff line number Diff line 
find_path(ZMQ_INCLUDE_DIR zmq.h)

find_library(ZMQ_LIBRARY NAMES zmq)



set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})

set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})



include(FindPackageHandleStandardArgs)

find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)

cmake/Modules/StyleHeaderUtils.cmake

+5 −0
Original line number Diff line number Diff line
@@ -48,8 +48,13 @@ function(CreateStyleHeader path filename) 
    set(temp "")

    if(ARGC GREATER 2)

        list(REMOVE_AT ARGV 0 1)

        set(header_list)

        foreach(FNAME ${ARGV})

            get_filename_component(FNAME ${FNAME} NAME)

            list(APPEND header_list ${FNAME})

        endforeach()

        list(SORT header_list)

        foreach(FNAME ${header_list})

            set(temp "${temp}#include \"${FNAME}\"\n")

        endforeach()

    endif()

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