Unverified Commit 7d0ac951 authored by Jacob Gissinger's avatar Jacob Gissinger Committed by GitHub
Browse files

Merge pull request #52 from lammps/master 

rebase
parents e8487ec0 1599fcef

cmake/CMakeLists.txt

+73 −13
Original line number Diff line number Diff line
@@ -37,7 +37,7 @@ include(PreventInSourceBuilds) 


if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)

  #release comes with -O3 by default

  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)

  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)

endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)

string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@@ -133,6 +133,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) 
  option(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()



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

# download and unpack support binaries for compilation

# of windows binaries.

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

if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")

  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"

          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)

  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")

    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")

  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")

    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")

  endif()

  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")

endif()



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

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

# packages with special compiler needs or external libs

######################################################
@@ -148,6 +166,7 @@ if(PKG_USER-ADIOS) 
endif()



# do MPI detection after language activation, if MPI for these language is required

set(MPI_CXX_SKIP_MPICXX TRUE)

find_package(MPI QUIET)

option(BUILD_MPI "Build MPI version" ${MPI_FOUND})

if(BUILD_MPI)
@@ -175,12 +194,14 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES}) 
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")



# posix_memalign is not available on Windows

if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

  set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)

else()

  set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")

endif()

if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")

  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})

endif()

endif()



option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)

if(LAMMPS_EXCEPTIONS)
@@ -219,8 +240,7 @@ if(BUILD_OMP) 
  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

endif()





if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)

  find_package(LAPACK)

  find_package(BLAS)

  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -230,6 +250,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI 
    enable_language(Fortran)

    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])

    add_library(linalg STATIC ${LAPACK_SOURCES})

    set(BLAS_LIBRARIES linalg)

    set(LAPACK_LIBRARIES linalg)

  else()

    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
@@ -497,10 +518,43 @@ if(BUILD_LIB) 
  if(LAMMPS_DEPS)

    add_dependencies(lammps ${LAMMPS_DEPS})

  endif()

  set(LAMMPS_CXX_HEADERS

    ${LAMMPS_SOURCE_DIR}/angle.h

    ${LAMMPS_SOURCE_DIR}/atom.h

    ${LAMMPS_SOURCE_DIR}/bond.h

    ${LAMMPS_SOURCE_DIR}/citeme.h

    ${LAMMPS_SOURCE_DIR}/comm.h

    ${LAMMPS_SOURCE_DIR}/compute.h

    ${LAMMPS_SOURCE_DIR}/dihedral.h

    ${LAMMPS_SOURCE_DIR}/domain.h

    ${LAMMPS_SOURCE_DIR}/error.h

    ${LAMMPS_SOURCE_DIR}/fix.h

    ${LAMMPS_SOURCE_DIR}/force.h

    ${LAMMPS_SOURCE_DIR}/group.h

    ${LAMMPS_SOURCE_DIR}/improper.h

    ${LAMMPS_SOURCE_DIR}/input.h

    ${LAMMPS_SOURCE_DIR}/kspace.h

    ${LAMMPS_SOURCE_DIR}/lammps.h

    ${LAMMPS_SOURCE_DIR}/lattice.h

    ${LAMMPS_SOURCE_DIR}/lmppython.h

    ${LAMMPS_SOURCE_DIR}/memory.h

    ${LAMMPS_SOURCE_DIR}/modify.h

    ${LAMMPS_SOURCE_DIR}/neighbor.h

    ${LAMMPS_SOURCE_DIR}/neigh_list.h

    ${LAMMPS_SOURCE_DIR}/output.h

    ${LAMMPS_SOURCE_DIR}/pair.h

    ${LAMMPS_SOURCE_DIR}/pointers.h

    ${LAMMPS_SOURCE_DIR}/region.h

    ${LAMMPS_SOURCE_DIR}/timer.h

    ${LAMMPS_SOURCE_DIR}/universe.h

    ${LAMMPS_SOURCE_DIR}/update.h

    ${LAMMPS_SOURCE_DIR}/variable.h)



  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)

  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)

  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)
@@ -535,6 +589,7 @@ if(BUILD_TOOLS) 
    enable_language(Fortran)

    add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)

    target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})

    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})

  endif()



  enable_language(C)
@@ -551,11 +606,11 @@ include(Documentation) 
###############################################################################

# Install potential and force field files in data directory

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

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

install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR})



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

install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR})

set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)

install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})

if(BUILD_TOOLS)

  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})

endif()



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)
@@ -673,5 +728,10 @@ if(PKG_KOKKOS) 
  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")

endif()

if(PKG_KSPACE)

  message(STATUS "Using ${FFT} as FFT")

  message(STATUS "Using ${FFT} as primary FFT library")

  if(FFT_SINGLE)

    message(STATUS "Using single precision FFTs")

  else()

    message(STATUS "Using double precision FFTs")

  endif()

endif()

cmake/Modules/Packages/KIM.cmake

+11 −4
Original line number Diff line number Diff line
@@ -9,6 +9,9 @@ if(PKG_KIM) 
  if(KIM-API_FOUND)

    set(DOWNLOAD_KIM_DEFAULT OFF)

  else()

    if (NOT DOWNLOAD_KIM)

      message(WARNING "KIM-API package not found.  We will download and build our own")

    endif()

    set(DOWNLOAD_KIM_DEFAULT ON)

  endif()

  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
@@ -17,12 +20,16 @@ if(PKG_KIM) 
      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")

    endif()

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

    enable_language(C)

    enable_language(Fortran)

    include(CheckLanguage)

    include(ExternalProject)

    enable_language(C)

    check_language(Fortran)

    if(NOT CMAKE_Fortran_COMPILER)

      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")

    endif()

    ExternalProject_Add(kim_build

      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz

      URL_MD5 537d9c0abd30f85b875ebb584f9143fa

      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz

      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8

      BINARY_DIR build

      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

cmake/Modules/Packages/KSPACE.cmake

+16 −12
Original line number Diff line number Diff line 
if(PKG_KSPACE)

  option(FFT_SINGLE "Use single precision FFT instead of double" OFF)

  option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)

  set(FFTW "FFTW3")

  if(FFT_SINGLE)

    set(FFTW "FFTW3F")
@@ -7,26 +7,30 @@ if(PKG_KSPACE) 
  endif()

  find_package(${FFTW} QUIET)

  if(${FFTW}_FOUND)

    set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")

    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")

  else()

    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")

  endif()

  set(FFT_VALUES KISS ${FFTW} MKL)

  set(FFT_VALUES KISS FFTW3 MKL)

  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})

  validate_option(FFT FFT_VALUES)

  string(TOUPPER ${FFT} FFT)

  if(NOT FFT STREQUAL "KISS")

    find_package(${FFT} REQUIRED)

    if(NOT FFT STREQUAL "FFTW3F")

      add_definitions(-DFFT_FFTW)

    else()

      add_definitions(-DFFT_${FFT})

    endif()

    include_directories(${${FFT}_INCLUDE_DIRS})

    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})



  if(FFT STREQUAL "FFTW3")

    find_package(${FFTW} REQUIRED)

    add_definitions(-DFFT_FFTW3)

    include_directories(${${FFTW}_INCLUDE_DIRS})

    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})

  elseif(FFT STREQUAL "MKL")

    find_package(MKL REQUIRED)

    add_definitions(-DFFT_MKL)

    include_directories(${MKL_INCLUDE_DIRS})

    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})

  else()

    # last option is KISSFFT

    add_definitions(-DFFT_KISS)

  endif()



  set(FFT_PACK "array" CACHE STRING "Optimization for FFT")

  set(FFT_PACK_VALUES array pointer memcpy)

  set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/USER-PLUMED.cmake

+19 −7
Original line number Diff line number Diff line 
if(PKG_USER-PLUMED)

  find_package(GSL REQUIRED)

  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")

  set(PLUMED_MODE_VALUES static shared runtime)

  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})

  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)

  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)



  set(PLUMED_LINK_LIBS "")

  if(PLUMED_MODE STREQUAL "STATIC")

    find_package(LAPACK REQUIRED)

    find_package(BLAS REQUIRED)

    find_package(GSL REQUIRED)

    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})

    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})

    find_package(ZLIB QUIET)

    if(ZLIB_FOUND)

      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})

    endif()

  endif()



  find_package(PkgConfig QUIET)

  set(DOWNLOAD_PLUMED_DEFAULT ON)

  if(PKG_CONFIG_FOUND)
@@ -37,8 +49,8 @@ if(PKG_USER-PLUMED) 
    message(STATUS "PLUMED download requested - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(plumed_build

      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz

      URL_MD5 c2a7b519e32197a120cdf47e0f194f81

      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz

      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

                                               ${CONFIGURE_REQUEST_PIC}
@@ -53,11 +65,11 @@ if(PKG_USER-PLUMED) 
    list(APPEND LAMMPS_DEPS plumed_build)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "SHARED")

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})

    endif()

    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
@@ -70,7 +82,7 @@ if(PKG_USER-PLUMED) 
    elseif(PLUMED_MODE STREQUAL "SHARED")

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)

    endif()

    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

cmake/Modules/Packages/VORONOI.cmake

+6 −2
Original line number Diff line number Diff line
@@ -18,8 +18,12 @@ if(PKG_VORONOI) 
    else()

      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")

    endif()

    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})

    if(APPLE)

      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)

      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})

    else()

      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})

    endif()



    ExternalProject_Add(voro_build

      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz

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