Unverified Commit fe2862d5 authored by Jacob Gissinger's avatar Jacob Gissinger Committed by GitHub
Browse files

Merge pull request #19 from lammps/master 

rebase
parents cfcb6902 ad3d049e

.github/CODEOWNERS

+12 −0
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ src/COMPRESS/* @akohlmey 
src/GPU/*             @ndtrung81

src/KOKKOS/*          @stanmoore1

src/KIM/*             @ellio167

src/LATTE/*           @cnegre

src/USER-CGDNA/*      @ohenrich

src/USER-CGSDK/*      @akohlmey

src/USER-COLVARS/*    @giacomofiorin
@@ -43,3 +44,14 @@ src/USER-MISC/*_grem.* @dstelter92 


# tools

tools/msi2lmp/*       @akohlmey



# cmake

cmake/*               @junghans @rbberger



# python

python/*              @rbberger



# docs

doc/utils/*/*         @rbberger

doc/Makefile          @rbberger

doc/README            @rbberger

cmake/CMakeLists.txt

+89 −47
Original line number Diff line number Diff line
@@ -2,9 +2,9 @@ 
# CMake build system

# This file is part of LAMMPS

# Created by Christoph Junghans and Richard Berger

cmake_minimum_required(VERSION 3.1)

cmake_minimum_required(VERSION 2.8.12)



project(lammps LANGUAGES CXX)

project(lammps CXX)

set(SOVERSION 0)

set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)

set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
@@ -49,6 +49,11 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") 
  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")

endif()



option(ENABLE_COVERAGE "Enable code coverage" OFF)

if(ENABLE_COVERAGE)

  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")

endif()



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

# User input options                                                   #

########################################################################
@@ -113,7 +118,7 @@ endif(ENABLE_TESTING) 
option(ENABLE_ALL "Build all default packages" OFF)

set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ

  REAX REPLICA RIGID SHOCK SNAP SRD)

  REAX REPLICA RIGID SHOCK SNAP SPIN SRD)

set(OTHER_PACKAGES 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
@@ -129,7 +134,7 @@ foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) 
endforeach()



macro(pkg_depends PKG1 PKG2)

  if(PKG_${PKG1} AND NOT PKG_${PKG2})

  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))

    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")

  endif()

endmacro()
@@ -137,10 +142,10 @@ endmacro() 
pkg_depends(MPIIO MPI)

pkg_depends(QEQ MANYBODY)

pkg_depends(USER-ATC MANYBODY)

pkg_depends(USER-H5MD MPI)

pkg_depends(USER-LB MPI)

pkg_depends(USER-MISC MANYBODY)

pkg_depends(USER-PHONON KSPACE)

pkg_depends(CORESHELL KSPACE)



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

# packages with special compiler needs or external libs
@@ -149,17 +154,10 @@ if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) 
  enable_language(Fortran)

endif()



if(PKG_MEAM)

if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)

  enable_language(C)

endif()



if(PKG_KOKKOS OR PKG_MSCG)

  # starting with CMake 3.1 this is all you have to do to enforce C++11

  set(CMAKE_CXX_STANDARD 11) # C++11...

  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...

  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11

endif()



find_package(OpenMP QUIET)

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

if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
@@ -203,7 +201,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) 
  find_package(LAPACK)

  if(NOT LAPACK_FOUND)

    enable_language(Fortran)

    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)

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

    add_library(linalg STATIC ${LAPACK_SOURCES})

    set(LAPACK_LIBRARIES linalg)

  endif()
@@ -298,8 +296,8 @@ if(PKG_LATTE) 
    message(STATUS "LATTE not found - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(latte_build

      URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz

      URL_MD5 cb86f1d2473ce00aa61ff6a023154b03

      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz

      URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb

      SOURCE_SUBDIR cmake

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}

      )
@@ -312,7 +310,7 @@ if(PKG_LATTE) 
      message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")

    endif()

  endif()

  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})

  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})

endif()



if(PKG_USER-MOLFILE)
@@ -336,13 +334,10 @@ if(PKG_USER-SMD) 
    ExternalProject_Add(Eigen3_build

      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz 

      URL_MD5 1a47e78efe365a97de0c022d127607c3

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DEIGEN_TEST_NOQT=ON

        -DCMAKE_DISABLE_FIND_PACKAGE_LAPACK=ON -DCMAKE_DISABLE_FIND_PACKAGE_Cholmod=ON -DCMAKE_DISABLE_FIND_PACKAGE_Umfpack=ON -DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=ON

        -DCMAKE_DISABLE_FIND_PACKAGE_PASTIX=ON -DCMAKE_DISABLE_FIND_PACKAGE_SPQR=ON -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON -DCMAKE_DISABLE_FIND_PACKAGE_CUDA=ON

        -DCMAKE_DISABLE_FIND_PACKAGE_FFTW=ON -DCMAKE_DISABLE_FIND_PACKAGE_MPFR=ON -DCMAKE_DISABLE_FIND_PACKAGE_OpenGL=ON

      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""

    )

    ExternalProject_get_property(Eigen3_build INSTALL_DIR)

    set(EIGEN3_INCLUDE_DIR ${INSTALL_DIR}/include/eigen3)

    ExternalProject_get_property(Eigen3_build SOURCE_DIR)

    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})

    list(APPEND LAMMPS_DEPS Eigen3_build)

  else()

    find_package(Eigen3)
@@ -355,14 +350,14 @@ endif() 


if(PKG_USER-QUIP)

  find_package(QUIP REQUIRED)

  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})

  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})

endif()



if(PKG_USER-QMMM)

  message(WARNING "Building QMMM with CMake is still experimental")

  find_package(QE REQUIRED)

  include_directories(${QE_INCLUDE_DIRS})

  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})

  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})

endif()



if(PKG_USER-VTK)
@@ -398,26 +393,36 @@ endif() 


if(PKG_MSCG)

  find_package(GSL REQUIRED)

  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)

  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)

  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)

  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})

    if(NOT EXISTS ${MSCG_TARBALL})

      message(STATUS "Downloading ${MSCG_TARBALL}")

      file(DOWNLOAD

        https://github.com/uchicago-voth/MSCG-release/archive/master.zip

        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master

    endif()

    message(STATUS "Unpacking ${MSCG_TARBALL}")

    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}

      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)

  endif()

  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)

  add_library(mscg STATIC ${MSCG_SOURCES})

  list(APPEND LAMMPS_LINK_LIBS mscg)

  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)

  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})

  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})

  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)

  if(DOWNLOAD_MSCG)

    include(ExternalProject)

    if(NOT LAPACK_FOUND)

      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")

    endif()

    ExternalProject_Add(mscg_build

      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz

      URL_MD5 8c45e269ee13f60b303edd7823866a91

      SOURCE_SUBDIR src/CMake

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}

      BUILD_COMMAND make mscg INSTALL_COMMAND ""

      )

    ExternalProject_get_property(mscg_build BINARY_DIR)

    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)

    ExternalProject_get_property(mscg_build SOURCE_DIR)

    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)

    list(APPEND LAMMPS_DEPS mscg_build)

    if(NOT LAPACK_FOUND)

      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})

      add_dependencies(mscg_build linalg)

    endif()

  else()

    find_package(MSCG)

    if(NOT MSCG_FOUND)

      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")

    endif()

  endif()

  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})

  include_directories(${MSCG_INCLUDE_DIRS})

endif()



if(PKG_COMPRESS)
@@ -657,6 +662,9 @@ if(PKG_USER-INTEL) 
endif()



if(PKG_GPU)

    if (CMAKE_VERSION VERSION_LESS "3.1") 

      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")

    endif()

    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)

    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h

                    ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -753,7 +761,7 @@ if(PKG_GPU) 
      add_library(gpu STATIC ${GPU_LIB_SOURCES})

      target_link_libraries(gpu ${OpenCL_LIBRARIES})

      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})

      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)

      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)

      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)



      list(APPEND LAMMPS_LINK_LIBS gpu)
@@ -793,6 +801,11 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR}) 
# Actually add executable and lib to build

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

add_library(lammps ${LIB_SOURCES})

get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)

list (FIND LANGUAGES "Fortran" _index)

if (${_index} GREATER -1)

  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})

endif()

list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)

target_link_libraries(lammps ${LAMMPS_LINK_LIBS})

if(LAMMPS_DEPS)
@@ -815,9 +828,38 @@ if(ENABLE_TESTING) 
  add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)

endif()



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

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

# Testing

#

# Requires latest gcovr (for GCC 8.1 support):#

# pip install git+https://github.com/gcovr/gcovr.git

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

if(ENABLE_COVERAGE)

    find_program(GCOVR_BINARY gcovr)

    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)



    if(GCOVR_FOUND)

        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)



        add_custom_target(

            gen_coverage_xml

            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml

            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}

            COMMENT "Generating XML Coverage Report..."

        )



        add_custom_target(

            gen_coverage_html

            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html

            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}

            COMMENT "Generating HTML Coverage Report..."

        )

    endif()

endif()



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

# Print package summary

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

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

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

  if(PKG_${PKG})

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

cmake/Modules/FindMSCG.cmake

0 → 100644
+22 −0
Original line number Diff line number Diff line 
# - Find mscg

# Find the native MSCG headers and libraries.

#

#  MSCG_INCLUDE_DIRS - where to find mscg.h, etc.

#  MSCG_LIBRARIES    - List of libraries when using mscg.

#  MSCG_FOUND        - True if mscg found.

#



find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)



find_library(MSCG_LIBRARY NAMES mscg)



set(MSCG_LIBRARIES ${MSCG_LIBRARY})

set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})



include(FindPackageHandleStandardArgs)

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

# if all listed variables are TRUE



find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)



mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/README.md

+1628 −10

File changed.

Preview size limit exceeded, changes collapsed.

doc/Makefile

+8 −1
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ TXT2RST = $(VENV)/bin/txt2rst 
ANCHORCHECK   = $(VENV)/bin/doc_anchor_check



PYTHON        = $(shell which python3)

VIRTUALENV     = virtualenv

HAS_PYTHON3    = NO

HAS_VIRTUALENV = NO
@@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0) 
HAS_PYTHON3 = YES

endif



ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)

VIRTUALENV     = virtualenv-3

HAS_VIRTUALENV = YES

endif



ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)

VIRTUALENV     = virtualenv

HAS_VIRTUALENV = YES

endif
@@ -158,7 +165,7 @@ $(VENV): 
	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi

	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi

	@( \

		virtualenv -p $(PYTHON) $(VENV); \

		$(VIRTUALENV) -p $(PYTHON) $(VENV); \

		. $(VENV)/bin/activate; \

		pip install Sphinx; \

		pip install sphinxcontrib-images; \

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