Unverified Commit 89886032 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1416 from akohlmey/collected-small-changes 

More collected small changes and bug fixes for next patch release
parents ce1040a1 cb559659

cmake/CMakeLists.txt

+78 −17
Original line number Diff line number Diff line
@@ -320,10 +320,15 @@ pkg_depends(USER-LB MPI) 
pkg_depends(USER-PHONON KSPACE)

pkg_depends(USER-SCAFACOS MPI)



include(CheckIncludeFileCXX)

find_package(OpenMP QUIET)

option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})

if(BUILD_OMP)

  find_package(OpenMP REQUIRED)

  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)

  if(NOT HAVE_OMP_H_INCLUDE)

    message(FATAL_ERROR "Cannot find required 'omp.h' header file")

  endif()

  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")

  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

endif()
@@ -443,7 +448,13 @@ endif() 




if(PKG_VORONOI)

  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)

  find_package(VORO)

  if(VORO_FOUND)

    set(DOWNLOAD_VORO_DEFAULT OFF)

  else()

    set(DOWNLOAD_VORO_DEFAULT ON)

  endif()

  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})

  if(DOWNLOAD_VORO)

    message(STATUS "Voro++ download requested - we will build our own")

    include(ExternalProject)
@@ -476,7 +487,13 @@ if(PKG_VORONOI) 
endif()



if(PKG_LATTE)

  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)

  find_package(LATTE)

  if(LATTE_FOUND)

    set(DOWNLOAD_LATTE_DEFAULT OFF)

  else()

    set(DOWNLOAD_LATTE_DEFAULT ON)

  endif()

  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})

  if(DOWNLOAD_LATTE)

    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR

      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
@@ -487,7 +504,7 @@ if(PKG_LATTE) 
      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz

      URL_MD5 85ac414fdada2d04619c8f936344df14

      SOURCE_SUBDIR cmake

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

    )

    ExternalProject_get_property(latte_build INSTALL_DIR)

    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
@@ -503,7 +520,15 @@ endif() 


if(PKG_USER-SCAFACOS)

  find_package(GSL REQUIRED)

  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)

  find_package(PkgConfig QUIET)

  set(DOWNLOAD_SCAFACOS_DEFAULT ON)

  if(PKG_CONFIG_FOUND)

    pkg_check_modules(SCAFACOS QUIET scafacos)

    if(SCAFACOS_FOUND)

      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)

    endif()

  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")

    include(ExternalProject)
@@ -543,8 +568,8 @@ if(PKG_USER-SCAFACOS) 
    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})

    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})

  else()

    FIND_PACKAGE(PkgConfig REQUIRED)

    PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)

    find_package(PkgConfig REQUIRED)

    pkg_check_modules(SCAFACOS REQUIRED scafacos)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})

  endif()

  include_directories(${SCAFACOS_INCLUDE_DIRS})
@@ -558,7 +583,16 @@ if(PKG_USER-PLUMED) 
  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)

  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)



  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)

  find_package(PkgConfig QUIET)

  set(DOWNLOAD_PLUMED_DEFAULT ON)

  if(PKG_CONFIG_FOUND)

    pkg_check_modules(PLUMED QUIET plumed)

    if(PLUMED_FOUND)

      set(DOWNLOAD_PLUMED_DEFAULT OFF)

    endif()

  endif()



  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})

  if(DOWNLOAD_PLUMED)

    if(BUILD_MPI)

      set(PLUMED_CONFIG_MPI "--enable-mpi")
@@ -603,7 +637,7 @@ if(PKG_USER-PLUMED) 
    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")

  else()

    find_package(PkgConfig REQUIRED)

    pkg_check_modules(PLUMED plumed REQUIRED)

    pkg_check_modules(PLUMED REQUIRED plumed)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
@@ -637,7 +671,13 @@ if(PKG_USER-NETCDF) 
endif()



if(PKG_USER-SMD)

  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)

  find_package(Eigen3 NO_MODULE)

  if(EIGEN3_FOUND)

    set(DOWNLOAD_EIGEN3_DEFAULT OFF)

  else()

    set(DOWNLOAD_EIGEN3_DEFAULT ON)

  endif()

  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})

  if(DOWNLOAD_EIGEN3)

    message(STATUS "Eigen3 download requested - we will build our own")

    include(ExternalProject)
@@ -685,7 +725,13 @@ if(PKG_KIM) 
    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})

    add_definitions(-DLMP_KIM_CURL)

  endif()

  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)

  find_package(KIM-API QUIET)

  if(KIM-API_FOUND)

    set(DOWNLOAD_KIM_DEFAULT OFF)

  else()

    set(DOWNLOAD_KIM_DEFAULT ON)

  endif()

  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})

  if(DOWNLOAD_KIM)

    message(STATUS "KIM-API download requested - we will build our own")

    enable_language(C)
@@ -706,10 +752,7 @@ if(PKG_KIM) 
    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})

    list(APPEND LAMMPS_DEPS kim_build)

  else()

    find_package(KIM-API)

    if(NOT KIM-API_FOUND)

      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")

    endif()

    find_package(KIM-API REQUIRED)

  endif()

  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")

  include_directories(${KIM-API_INCLUDE_DIRS})
@@ -747,7 +790,13 @@ endif() 


if(PKG_MSCG)

  find_package(GSL REQUIRED)

  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)

  find_package(MSCG QUIET)

  if(MSGC_FOUND)

    set(DOWNLOAD_MSCG_DEFAULT OFF)

  else()

    set(DOWNLOAD_MSCG_DEFAULT ON)

  endif()

  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})

  if(DOWNLOAD_MSCG)

    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR

      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@@ -796,7 +845,6 @@ endif() 
########################################################################

# Basic system tests (standard libraries, headers, functions, types)   #

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

include(CheckIncludeFileCXX)

foreach(HEADER cmath)

  check_include_file_cxx(${HEADER} FOUND_${HEADER})

  if(NOT FOUND_${HEADER})
@@ -1446,9 +1494,19 @@ if(BUILD_EXE) 
  if(ENABLE_TESTING)

    add_test(ShowHelp ${LAMMPS_BINARY} -help)

  endif()



  enable_language(C)

  get_filename_component(MSI2LMP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools/msi2lmp/src ABSOLUTE)

  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)

  add_executable(msi2lmp ${MSI2LMP_SOURCES})

  target_link_libraries(msi2lmp m)

  install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})

  install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)



endif()







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

# Build documentation

###############################################################################
@@ -1510,11 +1568,14 @@ if(BUILD_DOC) 
endif()



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

# Install potential files in data directory

# Install potential and force field files in data directory

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

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

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



set(LAMMPS_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)

install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../tools/msi2lmp/frc_files/ DESTINATION ${LAMMPS_FRC_FILES_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)

install(

cmake/Modules/FindKIM-API.cmake

+14 −5
Original line number Diff line number Diff line
@@ -36,14 +36,23 @@ 
# KIM-API-CMAKE_CXX_COMPILER

# KIM-API-CMAKE_Fortran_COMPILER

#

find_package(PkgConfig REQUIRED)



if(KIM-API_FIND_QUIETLY)

  set(REQ_OR_QUI "QUIET")

else()

  set(REQ_OR_QUI "REQUIRED")

endif()



find_package(PkgConfig ${REQ_OR_QUI})

include(FindPackageHandleStandardArgs)



pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)

pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)



pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)

pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)

pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)

if(KIM-API_FOUND)

  pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)

  pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)

  pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)

endif()



# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE

# if all listed variables are TRUE

cmake/etc/profile.d/lammps.csh.in

+3 −1
Original line number Diff line number Diff line 
# set environment for LAMMPS executables to find potential files

# set environment for LAMMPS and msi2lmp executables

# to find potential and force field files

if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@

if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@

cmake/etc/profile.d/lammps.sh.in

+5 −2
Original line number Diff line number Diff line 
# set environment for LAMMPS executables to find potential files

export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
 
# set environment for LAMMPS and msi2lmp executables

# to find potential and force field files

LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}

MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}

export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

cmake/presets/clang.cmake

0 → 100644
+17 −0
Original line number Diff line number Diff line 
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)



set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)

set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)

set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)

set(MPI_CXX "clang++" CACHE STRING "" FORCE)

set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)

unset(HAVE_OMP_H_INCLUDE CACHE)



set(OpenMP_C "clang" CACHE STRING "" FORCE)

set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)

set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)

set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)

set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)

set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)

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