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Merge branch 'master' into gran_attractive

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This commit is contained in:
Joel Clemmer
2021-04-06 13:11:37 -06:00
parent 80a65150c2 00e4bdb2b7
commit 6294a7c0dd
42 changed files with 522 additions and 148 deletions
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4
.github/workflows/unittest-macos.yml vendored
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@ -24,7 +24,9 @@ jobs:
shell: bash shell: bash
working-directory: ${{github.workspace}}/build working-directory: ${{github.workspace}}/build
run: | run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \ cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
-C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
$GITHUB_WORKSPACE/cmake \
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
cmake --build . --parallel 2 cmake --build . --parallel 2

5
cmake/CMakeLists.txt
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@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools)
set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python) set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python)
set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials) set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty")
mark_as_advanced(LAMMPS_DOWNLOADS_URL)
find_package(Git) find_package(Git)
# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed

8
cmake/Modules/Documentation.cmake
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@ -55,11 +55,15 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
) )
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
# download mathjax distribution and unpack to folder "mathjax" # download mathjax distribution and unpack to folder "mathjax"
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5) if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" file(DOWNLOAD ${MATHJAX_URL}
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53) EXPECTED_MD5 ${MATHJAX_MD5})
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) 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-*) file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

6
cmake/Modules/GTest.cmake
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@ -8,10 +8,12 @@ endif()
include(ExternalProject) include(ExternalProject)
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball") set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
mark_as_advanced(GTEST_URL) mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
ExternalProject_Add(googletest ExternalProject_Add(googletest
URL ${GTEST_URL} URL ${GTEST_URL}
URL_MD5 ecd1fa65e7de707cd5c00bdac56022cd URL_MD5 ${GTEST_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src" SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build" BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS} CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

1
cmake/Modules/LAMMPSUtils.cmake
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@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
# fetch missing potential files # fetch missing potential files
function(FetchPotentials pkgfolder potfolder) function(FetchPotentials pkgfolder potfolder)
if (EXISTS "${pkgfolder}/potentials.txt") if (EXISTS "${pkgfolder}/potentials.txt")
set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].") file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist}) foreach(line ${linelist})
string(FIND ${line} " " blank) string(FIND ${line} " " blank)

17
cmake/Modules/MPI4WIN.cmake
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@ -1,16 +1,25 @@
# Download and configure custom MPICH files for Windows # Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject) include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build ExternalProject_Add(mpi4win_build
URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 4939fdb59d13182fd5dd65211e469f14 URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a) BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else() else()
ExternalProject_Add(mpi4win_build ExternalProject_Add(mpi4win_build
URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 a61d153500dce44e21b755ee7257e031 URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a) BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif() endif()

10
cmake/Modules/OpenCLLoader.cmake
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@ -1,11 +1,13 @@
message(STATUS "Downloading and building OpenCL loader library") message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)
include(ExternalProject) include(ExternalProject)
set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
ExternalProject_Add(opencl_loader ExternalProject_Add(opencl_loader
URL ${OPENCL_LOADER_URL} URL ${OPENCL_LOADER_URL}
URL_MD5 011cdcbd41030be94f3fced6d763a52a URL_MD5 ${OPENCL_LOADER_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src" SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build" BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS} CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}

23
cmake/Modules/Packages/GPU.cmake
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@ -218,7 +218,7 @@ elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PLATFORM) if(NOT DEFINED HIP_PLATFORM)
if(NOT DEFINED ENV{HIP_PLATFORM}) if(NOT DEFINED ENV{HIP_PLATFORM})
set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation") set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation")
else() else()
set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation") set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
endif() endif()
@ -226,7 +226,7 @@ elseif(GPU_API STREQUAL "HIP")
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM}) set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
if(HIP_PLATFORM STREQUAL "hcc") if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture") set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc") elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED) find_package(CUDA REQUIRED)
@ -284,7 +284,7 @@ elseif(GPU_API STREQUAL "HIP")
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
if(HIP_PLATFORM STREQUAL "hcc") if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
if(HIP_COMPILER STREQUAL "clang") if(HIP_COMPILER STREQUAL "clang")
@ -338,11 +338,16 @@ elseif(GPU_API STREQUAL "HIP")
if(DOWNLOAD_CUB) if(DOWNLOAD_CUB)
message(STATUS "CUB download requested") message(STATUS "CUB download requested")
set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
mark_as_advanced(CUB_URL)
mark_as_advanced(CUB_MD5)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(CUB ExternalProject_Add(CUB
GIT_REPOSITORY https://github.com/NVlabs/cub URL ${CUB_URL}
TIMEOUT 5 URL_MD5 ${CUB_MD5}
PREFIX "${CMAKE_CURRENT_BINARY_DIR}" PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
CONFIGURE_COMMAND "" CONFIGURE_COMMAND ""
BUILD_COMMAND "" BUILD_COMMAND ""
@ -354,7 +359,7 @@ elseif(GPU_API STREQUAL "HIP")
else() else()
find_package(CUB) find_package(CUB)
if(NOT CUB_FOUND) if(NOT CUB_FOUND)
message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it")
endif() endif()
endif() endif()
@ -381,6 +386,12 @@ elseif(GPU_API STREQUAL "HIP")
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__) target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
elseif(HIP_PLATFORM STREQUAL "amd")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
endif() endif()
target_link_libraries(lammps PRIVATE gpu) target_link_libraries(lammps PRIVATE gpu)

8
cmake/Modules/Packages/KIM.cmake
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@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
include(ExternalProject) include(ExternalProject)
enable_language(C) enable_language(C)
enable_language(Fortran) enable_language(Fortran)
set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
mark_as_advanced(KIM_URL)
mark_as_advanced(KIM_MD5)
ExternalProject_Add(kim_build ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz URL ${KIM_URL}
URL_MD5 ae1ddda2ef7017ea07934e519d023dca URL_MD5 ${KIM_MD5}
BINARY_DIR build BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC} CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

8
cmake/Modules/Packages/KOKKOS.cmake
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@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}") list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject) include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build ExternalProject_Add(kokkos_build
URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz URL ${KOKKOS_URL}
URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS} CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
) )

8
cmake/Modules/Packages/LATTE.cmake
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@ -15,10 +15,14 @@ endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT}) option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE) if(DOWNLOAD_LATTE)
message(STATUS "LATTE download requested - we will build our own") message(STATUS "LATTE download requested - we will build our own")
set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
mark_as_advanced(LATTE_URL)
mark_as_advanced(LATTE_MD5)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(latte_build ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz URL ${LATTE_URL}
URL_MD5 820e73a457ced178c08c71389a385de7 URL_MD5 ${LATTE_MD5}
SOURCE_SUBDIR cmake SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

9
cmake/Modules/Packages/MSCG.cmake
View File

@ -7,10 +7,15 @@ else()
endif() endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT}) option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG) if(DOWNLOAD_MSCG)
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(mscg_build ExternalProject_Add(mscg_build
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz URL ${MSCG_URL}
URL_MD5 8c45e269ee13f60b303edd7823866a91 URL_MD5 ${MSCG_MD5}
SOURCE_SUBDIR src/CMake SOURCE_SUBDIR src/CMake
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS} CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

10
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -53,10 +53,16 @@ if(DOWNLOAD_PLUMED)
elseif(PLUMED_MODE STREQUAL "RUNTIME") elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a") set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif() endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(plumed_build ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz URL ${PLUMED_URL}
URL_MD5 95f29dd0c067577f11972ff90dfc7d12 URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1 BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC} ${CONFIGURE_REQUEST_PIC}

10
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -14,15 +14,19 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS) if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own") message(STATUS "ScaFaCoS download requested - we will build our own")
set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
mark_as_advanced(SCAFACOS_URL)
mark_as_advanced(SCAFACOS_MD5)
# version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later. # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032) EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(scafacos_build ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz URL ${SCAFACOS_URL}
URL_MD5 bd46d74e3296bd8a444d731bb10c1738 URL_MD5 ${SCAFACOS_MD5}
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

8
cmake/Modules/Packages/USER-SMD.cmake
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@ -7,10 +7,14 @@ endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT}) option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3) if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own") message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
mark_as_advanced(EIGEN3_URL)
mark_as_advanced(EIGEN3_MD5)
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(Eigen3_build ExternalProject_Add(Eigen3_build
URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz URL ${EIGEN3_URL}
URL_MD5 9e30f67e8531477de4117506fe44669b URL_MD5 ${EIGEN3_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
) )
ExternalProject_get_property(Eigen3_build SOURCE_DIR) ExternalProject_get_property(Eigen3_build SOURCE_DIR)

9
cmake/Modules/Packages/VORONOI.cmake
View File

@ -7,6 +7,11 @@ endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT}) option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO) if(DOWNLOAD_VORO)
message(STATUS "Voro++ download requested - we will build our own") message(STATUS "Voro++ download requested - we will build our own")
set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball")
set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball")
mark_as_advanced(VORO_URL)
mark_as_advanced(VORO_MD5)
include(ExternalProject) include(ExternalProject)
if(BUILD_SHARED_LIBS) if(BUILD_SHARED_LIBS)
@ -22,8 +27,8 @@ if(DOWNLOAD_VORO)
endif() endif()
ExternalProject_Add(voro_build ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz URL ${VORO_URL}
URL_MD5 2338b824c3b7b25590e18e8df5d68af9 URL_MD5 ${VORO_MD5}
PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
CONFIGURE_COMMAND "" CONFIGURE_COMMAND ""
BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_COMMAND make ${VORO_BUILD_OPTIONS}

5
cmake/Modules/YAML.cmake
View File

@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library")
include(ExternalProject) include(ExternalProject)
set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball") set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
mark_as_advanced(YAML_URL) mark_as_advanced(YAML_URL)
mark_as_advanced(YAML_MD5)
ExternalProject_Add(libyaml ExternalProject_Add(libyaml
URL ${YAML_URL} URL ${YAML_URL}
URL_MD5 bb15429d8fb787e7d3f1c83ae129a999 URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src" SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build" BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC} CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}

13
doc/src/Build_extras.rst
View File

@ -125,7 +125,7 @@ CMake build
# default is sm_50 # default is sm_50
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip -D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM # value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no # value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs) -D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
@ -169,17 +169,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling with HIP, note that before running CMake you will have to If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc` :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly. and the linker to work correctly.
.. code:: bash .. code:: bash
# AMDGPU target # AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906 export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4 make -j 4
.. code:: bash
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash .. code:: bash
# CUDA target (not recommended, use GPU_ARCH=cuda) # CUDA target (not recommended, use GPU_ARCH=cuda)

45
doc/src/Developer_unittest.rst
View File

@ -4,10 +4,10 @@ Adding tests for unit testing
This section discusses adding or expanding tests for the unit test This section discusses adding or expanding tests for the unit test
infrastructure included into the LAMMPS source code distribution. infrastructure included into the LAMMPS source code distribution.
Unlike example inputs, unit tests focus on testing the "local" behavior Unlike example inputs, unit tests focus on testing the "local" behavior
of individual features, tend to run very fast, and should be set up to of individual features, tend to run fast, and should be set up to cover
cover as much of the added code as possible. When contributing code to as much of the added code as possible. When contributing code to the
the distribution, the LAMMPS developers will appreciate if additions distribution, the LAMMPS developers will appreciate if additions to the
to the integrated unit test facility are included. integrated unit test facility are included.
Given the complex nature of MD simulations where many operations can Given the complex nature of MD simulations where many operations can
only be performed when suitable "real" simulation environment has been only be performed when suitable "real" simulation environment has been
@ -50,6 +50,9 @@ available:
* - File name: * - File name:
- Test name: - Test name:
- Description: - Description:
* - ``test_argutils.cpp``
- ArgInfo
- Tests for ``ArgInfo`` class used by LAMMPS
* - ``test_fmtlib.cpp`` * - ``test_fmtlib.cpp``
- FmtLib - FmtLib
- Tests for ``fmtlib::`` functions used by LAMMPS - Tests for ``fmtlib::`` functions used by LAMMPS
@ -155,23 +158,27 @@ have the desired effect:
{ {
ASSERT_EQ(lmp->update->ntimestep, 0); ASSERT_EQ(lmp->update->ntimestep, 0);
if (!verbose) ::testing::internal::CaptureStdout(); BEGIN_HIDE_OUTPUT();
lmp->input->one("reset_timestep 10"); command("reset_timestep 10");
if (!verbose) ::testing::internal::GetCapturedStdout(); END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10); ASSERT_EQ(lmp->update->ntimestep, 10);
if (!verbose) ::testing::internal::CaptureStdout(); BEGIN_HIDE_OUTPUT();
lmp->input->one("reset_timestep 0"); command("reset_timestep 0");
if (!verbose) ::testing::internal::GetCapturedStdout(); END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 0); ASSERT_EQ(lmp->update->ntimestep, 0);
TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
} }
Please note the use of the (global) verbose variable to control whether Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
the LAMMPS command will be silent by capturing the output or not. In functions that will capture output from running LAMMPS. This is normally
the default case, verbose == false, the test output will be compact and discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
not mixed with LAMMPS output. However setting the verbose flag (via environment variable, ``TEST_ARGS=-v``) it can be printed and used to
setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be understand why tests fail unexpectedly.
helpful to understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called situations where LAMMPS will stop with an error, i.e. handle so-called
@ -210,6 +217,12 @@ The following test programs are currently available:
* - ``test_lattice_region.cpp`` * - ``test_lattice_region.cpp``
- LatticeRegion - LatticeRegion
- Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
* - ``test_groups.cpp``
- GroupTest
- Tests to validate the :doc:`group <group>` command
* - ``test_variables.cpp``
- VariableTest
- Tests to validate the :doc:`variable <variable>` command
* - ``test_kim_commands.cpp`` * - ``test_kim_commands.cpp``
- KimCommands - KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>` - Tests for several commands from the :ref:`KIM package <PKG-KIM>`

2
doc/src/Packages_standard.rst
View File

@ -71,6 +71,8 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no | | :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUGIN <PKG-PLUGIN>` | Plugin loader command | :doc:`plugin <plugin>` | plugins | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int | | :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys | | :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |

9
doc/src/rerun.rst
View File

@ -15,7 +15,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump* keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump*
*first* args = Nfirst *first* args = Nfirst
Nfirst = dump timestep to start on Nfirst = dump timestep to start on
*last* args = Nlast *last* args = Nlast
@ -28,6 +28,7 @@ Syntax
Nstart = timestep on which pseudo run will start Nstart = timestep on which pseudo run will start
*stop* args = Nstop *stop* args = Nstop
Nstop = timestep to which pseudo run will end Nstop = timestep to which pseudo run will end
*post* value = *yes* or *no*
*dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments *dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments
Examples Examples
@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the
dump file with a timestep value larger than the *stop* setting you dump file with a timestep value larger than the *stop* setting you
have specified. have specified.
The *post* keyword can be used to minimize the output to the screen that
happens after a *rerun* command, similar to the post keyword of the
:doc:`run command <run>`. It is set to *no* by default.
The *dump* keyword is required and must be the last keyword specified. The *dump* keyword is required and must be the last keyword specified.
Its arguments are passed internally to the :doc:`read_dump <read_dump>` Its arguments are passed internally to the :doc:`read_dump <read_dump>`
command. The first argument following the *dump* keyword should be command. The first argument following the *dump* keyword should be
@ -226,4 +231,4 @@ Default
The option defaults are first = 0, last = a huge value (effectively The option defaults are first = 0, last = a huge value (effectively
infinity), start = same as first, stop = same as last, every = 0, skip infinity), start = same as first, stop = same as last, every = 0, skip
= 1; = 1, post = no;

6
lib/gpu/Makefile.hip
View File

@ -1,6 +1,6 @@
# /* ---------------------------------------------------------------------- # /* ----------------------------------------------------------------------
# Generic Linux Makefile for HIP # Generic Linux Makefile for HIP
# - export HIP_PLATFORM=hcc (or nvcc) before execution # - export HIP_PLATFORM=amd (or nvcc) before execution
# - change HIP_ARCH for your GPU # - change HIP_ARCH for your GPU
# ------------------------------------------------------------------------- */ # ------------------------------------------------------------------------- */
@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906 # possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906 HIP_ARCH = gfx906
else ifeq (amd,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (nvcc,$(HIP_PLATFORM)) else ifeq (nvcc,$(HIP_PLATFORM))
HIP_OPTS += --use_fast_math HIP_OPTS += --use_fast_math
HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \ HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \

5
lib/gpu/README
View File

@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and
extract the cub directory to lammps/lib/gpu/ or specify an appropriate extract the cub directory to lammps/lib/gpu/ or specify an appropriate
path in lammps/lib/gpu/Makefile.hip. path in lammps/lib/gpu/Makefile.hip.
2. In Makefile.hip it is possible to specify the target platform via 2. In Makefile.hip it is possible to specify the target platform via
export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0)
architecture (gfx803, gfx900, gfx906 etc.) or HIP_PLATFORM=nvcc as well as the target architecture (gfx803, gfx900, gfx906 etc.)
3. If your MPI implementation does not support `mpicxx --showme` command, 3. If your MPI implementation does not support `mpicxx --showme` command,
it is required to specify the corresponding MPI compiler and linker flags it is required to specify the corresponding MPI compiler and linker flags
in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip. in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip.
@ -278,4 +278,3 @@ and
Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High
Performance Computers - Three-Body Potentials. Computer Physics Communications. Performance Computers - Three-Body Potentials. Computer Physics Communications.
2013. 184: p. 2785–2793. 2013. 184: p. 2785–2793.

8
lib/gpu/lal_pre_cuda_hip.h
View File

@ -30,7 +30,7 @@
// ------------------------------------------------------------------------- // -------------------------------------------------------------------------
#ifdef __HIP_PLATFORM_HCC__ #if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#define CONFIG_ID 303 #define CONFIG_ID 303
#define SIMD_SIZE 64 #define SIMD_SIZE 64
#else #else
@ -161,7 +161,7 @@
// KERNEL MACROS - TEXTURES // KERNEL MACROS - TEXTURES
// ------------------------------------------------------------------------- // -------------------------------------------------------------------------
#ifdef __HIP_PLATFORM_HCC__ #if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#define _texture(name, type) __device__ type* name #define _texture(name, type) __device__ type* name
#define _texture_2d(name, type) __device__ type* name #define _texture_2d(name, type) __device__ type* name
#else #else
@ -201,7 +201,7 @@
#define mu_tex mu_ #define mu_tex mu_
#endif #endif
#ifdef __HIP_PLATFORM_HCC__ #if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#undef fetch4 #undef fetch4
#undef fetch #undef fetch
@ -266,7 +266,7 @@ typedef struct _double4 double4;
#endif #endif
#endif #endif
#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) #if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
#ifdef _SINGLE_SINGLE #ifdef _SINGLE_SINGLE
#define shfl_down __shfl_down #define shfl_down __shfl_down

16
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -17,21 +17,21 @@
#include "pair_lj_cut_coul_long.h" #include "pair_lj_cut_coul_long.h"
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "error.h"
#include "force.h" #include "force.h"
#include "kspace.h" #include "kspace.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;

45
src/USER-REAXC/reaxc_tool_box.cpp
View File

@ -25,10 +25,11 @@
----------------------------------------------------------------------*/ ----------------------------------------------------------------------*/
#include "reaxc_tool_box.h" #include "reaxc_tool_box.h"
#include "reaxc_defs.h"
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "reaxc_defs.h"
#include "error.h" #include "error.h"
@ -49,62 +50,58 @@ int Tokenize( char* s, char*** tok )
return count; return count;
} }
/* safe malloc */ /* safe malloc */
void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name ) void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name )
{ {
void *ptr; void *ptr;
char errmsg[256];
if (n <= 0) { if (n <= 0) {
snprintf(errmsg, 256, "Trying to allocate %ld bytes for array %s. " auto errmsg = fmt::format("Trying to allocate {} bytes for array {}. "
"returning NULL.", n, name); "returning NULL.", n, name);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
return nullptr; return nullptr;
} }
ptr = malloc( n ); ptr = malloc( n );
if (ptr == nullptr) { if (ptr == nullptr) {
snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n, name); auto errmsg = fmt::format("Failed to allocate {} bytes for array {}",
n, name);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
} }
return ptr; return ptr;
} }
/* safe calloc */ /* safe calloc */
void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name ) void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name )
{ {
void *ptr; void *ptr;
char errmsg[256];
if (n <= 0) { if (n <= 0) {
snprintf(errmsg, 256, "Trying to allocate %ld elements for array %s. " auto errmsg = fmt::format("Trying to allocate {} elements for array {}. "
"returning NULL.\n", n, name ); "returning NULL.\n", n, name);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
return nullptr; return nullptr;
} }
if (size <= 0) { if (size <= 0) {
snprintf(errmsg, 256, "Elements size for array %s is %ld. " auto errmsg = fmt::format("Elements size for array {} is {}. "
"returning NULL", name, size ); "returning NULL", name, size);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
return nullptr; return nullptr;
} }
ptr = calloc( n, size ); ptr = calloc( n, size );
if (ptr == nullptr) { if (ptr == nullptr) {
char errmsg[256]; auto errmsg = fmt::format("Failed to allocate {} bytes for array {}",
snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n*size, name); n*size, name);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
} }
return ptr; return ptr;
@ -115,14 +112,14 @@ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const c
void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name ) void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name )
{ {
if (ptr == nullptr) { if (ptr == nullptr) {
char errmsg[256]; auto errmsg = fmt::format("Trying to free the already free()'d pointer {}",
snprintf(errmsg, 256, "Trying to free the already NULL pointer %s", name ); name);
if (error_ptr) error_ptr->one(FLERR,errmsg); if (error_ptr) error_ptr->one(FLERR,errmsg);
else fputs(errmsg,stderr); else fputs(errmsg.c_str(),stderr);
return; return;
} }
free( ptr ); free(ptr);
ptr = nullptr; ptr = nullptr;
} }

16
src/USER-REAXC/reaxc_traj.h
View File

@ -36,14 +36,18 @@
#define HEADER_LINE_LEN 62 #define HEADER_LINE_LEN 62
#define STR_LINE "%-37s%-24s\n" #define STR_LINE "%-37s%-24s\n"
#define INT_LINE "%-37s%-24d\n" #define INT_LINE "%-37s%-24d\n"
#define BIGINT_LINE "%-37s%-24ld\n" #if defined(LAMMPS_SMALLSMALL)
#define BIGINT_LINE "%-37s%-24d\n"
#else
#define BIGINT_LINE "%-37s%-24lld\n"
#endif
#define INT2_LINE "%-36s%-12d,%-12d\n" #define INT2_LINE "%-36s%-12d,%-12d\n"
#define REAL_LINE "%-37s%-24.3f\n" #define REAL_LINE "%-37s%-24.3f\n"
#define SCI_LINE "%-37s%-24g\n" #define SCI_LINE "%-37s%-24g\n"
#define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n" #define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n"
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
#define INIT_DESC "%9ld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass #define INIT_DESC "%9lld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
#else #else
#define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass #define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
#endif #endif
@ -56,7 +60,7 @@
#define SIZE_INFO_LEN3 31 #define SIZE_INFO_LEN3 31
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
#define ATOM_BASIC "%9ld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge #define ATOM_BASIC "%9lld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
#define ATOM_wV "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge #define ATOM_wV "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
#define ATOM_wF "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge #define ATOM_wF "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
#define ATOM_FULL "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge #define ATOM_FULL "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
@ -72,9 +76,9 @@
#define ATOM_FULL_LEN 110 #define ATOM_FULL_LEN 110
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
#define BOND_BASIC "%9ld%9ld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO #define BOND_BASIC "%9lld%9lld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
#define BOND_FULL "%9ld%9ld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 #define BOND_FULL "%9lld%9lld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
#define ANGLE_BASIC "%9ld%9ld%9ld%10.3f\n" // Atom1 Atom2 Atom3 Theta #define ANGLE_BASIC "%9lld%9lld%9lld%10.3f\n" // Atom1 Atom2 Atom3 Theta
#else #else
#define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO #define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
#define BOND_FULL "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2 #define BOND_FULL "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2

22
src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
View File

@ -106,6 +106,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
firstneigh = list->firstneigh; firstneigh = list->firstneigh;
// loop over neighbors of my atoms // loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) { for (ii = 0; ii < inum; ii++) {
i = ilist[ii]; i = ilist[ii];
qtmp = q[i]; qtmp = q[i];
@ -193,7 +194,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
offset[itype][jtype]; offset[itype][jtype];
} else evdwl = 0.0; } else evdwl = 0.0;
// Truncation, see Yaff Switch33 // Truncation, see Yaff Switch3
if (truncw>0) { if (truncw>0) {
if (rsq < cut_ljsq[itype][jtype]) { if (rsq < cut_ljsq[itype][jtype]) {
if (r>cut_lj[itype][jtype]-truncw) { if (r>cut_lj[itype][jtype]-truncw) {
@ -262,19 +263,18 @@ void PairLJSwitch3CoulGaussLong::allocate()
void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg) void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg)
{ {
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp); cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
if (narg == 2) { if (narg == 2) {
cut_coul = cut_lj_global; cut_coul = cut_lj_global;
truncw = utils::numeric(FLERR,arg[1],false,lmp); truncw = utils::numeric(FLERR,arg[1],false,lmp);
} } else {
else {
cut_coul = utils::numeric(FLERR,arg[1],false,lmp); cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
truncw = utils::numeric(FLERR,arg[2],false,lmp); truncw = utils::numeric(FLERR,arg[2],false,lmp);
} }
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// reset cutoffs that have been explicitly set // reset cutoffs that have been explicitly set
if (allocated) { if (allocated) {
@ -332,6 +332,9 @@ void PairLJSwitch3CoulGaussLong::init_style()
cut_coulsq = cut_coul * cut_coul; cut_coulsq = cut_coul * cut_coul;
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// insure use of KSpace long-range solver, set g_ewald // insure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) if (force->kspace == nullptr)
@ -375,8 +378,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
double r6inv = r2inv*r2inv*r2inv; double r6inv = r2inv*r2inv*r2inv;
double r12inv = r6inv*r6inv; double r12inv = r6inv*r6inv;
offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv; offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv;
} } else {offset[i][j] = 0.0;}
else {offset[i][j] = 0.0;}
} else offset[i][j] = 0.0; } else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j]; cut_ljsq[j][i] = cut_ljsq[i][j];
@ -431,8 +433,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9; double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9;
etail_ij = 2.0*MY_PI*all[0]*all[1]*t71; etail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71; ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
} } else {
else {
double t1 = pow(cg3, 0.2e1); double t1 = pow(cg3, 0.2e1);
double t2 = t1 * t1; double t2 = t1 * t1;
double t3 = t2 * t1; double t3 = t2 * t1;
@ -618,6 +619,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
expn2 = 0.0; expn2 = 0.0;
erfc2 = 0.0; erfc2 = 0.0;
forcecoul2 = 0.0; forcecoul2 = 0.0;
prefactor2 = 0.0;
} else { } else {
r = sqrt(rsq); r = sqrt(rsq);
rrij = lj2[itype][jtype]*r; rrij = lj2[itype][jtype]*r;

20
src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
View File

@ -106,6 +106,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
firstneigh = list->firstneigh; firstneigh = list->firstneigh;
// loop over neighbors of my atoms // loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) { for (ii = 0; ii < inum; ii++) {
i = ilist[ii]; i = ilist[ii];
qtmp = q[i]; qtmp = q[i];
@ -170,6 +171,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
expn2 = 0.0; expn2 = 0.0;
erfc2 = 0.0; erfc2 = 0.0;
forcecoul2 = 0.0; forcecoul2 = 0.0;
prefactor2 = 0.0;
} else { } else {
rrij = lj2[itype][jtype]*r; rrij = lj2[itype][jtype]*r;
expn2 = exp(-rrij*rrij); expn2 = exp(-rrij*rrij);
@ -263,19 +265,18 @@ void PairMM3Switch3CoulGaussLong::allocate()
void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg) void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg)
{ {
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp); cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
if (narg == 2) { if (narg == 2) {
cut_coul = cut_lj_global; cut_coul = cut_lj_global;
truncw = utils::numeric(FLERR,arg[1],false,lmp); truncw = utils::numeric(FLERR,arg[1],false,lmp);
} } else {
else {
cut_coul = utils::numeric(FLERR,arg[1],false,lmp); cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
truncw = utils::numeric(FLERR,arg[2],false,lmp); truncw = utils::numeric(FLERR,arg[2],false,lmp);
} }
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// reset cutoffs that have been explicitly set // reset cutoffs that have been explicitly set
if (allocated) { if (allocated) {
@ -333,6 +334,9 @@ void PairMM3Switch3CoulGaussLong::init_style()
cut_coulsq = cut_coul * cut_coul; cut_coulsq = cut_coul * cut_coul;
if (truncw>0.0) truncwi = 1.0/truncw;
else truncwi = 0.0;
// insure use of KSpace long-range solver, set g_ewald // insure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) if (force->kspace == nullptr)
@ -375,8 +379,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
double r6inv = r2inv*r2inv*r2inv; double r6inv = r2inv*r2inv*r2inv;
double expb = lj3[i][j]*exp(-lj1[i][j]*r); double expb = lj3[i][j]*exp(-lj1[i][j]*r);
offset[i][j] = expb-lj4[i][j]*r6inv; offset[i][j] = expb-lj4[i][j]*r6inv;
} } else {offset[i][j] = 0.0;}
else {offset[i][j] = 0.0;}
} else offset[i][j] = 0.0; } else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j]; cut_ljsq[j][i] = cut_ljsq[i][j];
@ -426,8 +429,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39); double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39);
etail_ij = 2.0*MY_PI*all[0]*all[1]*t64; etail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64; ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
} } else {
else {
double t2 = pow(cg3, 0.2e1); double t2 = pow(cg3, 0.2e1);
double t3 = t2 * t2; double t3 = t2 * t2;
double t7 = 0.12e2 / cg3 * cg1; double t7 = 0.12e2 / cg3 * cg1;

11
src/random_mars.cpp
View File

@ -136,13 +136,16 @@ double RanMars::gaussian(double mu, double sigma)
double RanMars::rayleigh(double sigma) double RanMars::rayleigh(double sigma)
{ {
double first,v1; double v1;
if (sigma <= 0) error->all(FLERR,"Invalid Rayleigh parameter"); if (sigma <= 0.0) error->all(FLERR,"Invalid Rayleigh parameter");
v1 = uniform(); v1 = uniform();
first = sigma*sqrt(-2.0*log(v1)); // avoid a floating point exception due to log(0.0)
return first; // and just return a very big number
if (v1 == 0.0) return 1.0e300;
return sigma*sqrt(-2.0*log(v1));
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

12
src/rerun.cpp
View File

@ -51,6 +51,7 @@ void Rerun::command(int narg, char **arg)
if (strcmp(arg[iarg],"start") == 0) break; if (strcmp(arg[iarg],"start") == 0) break;
if (strcmp(arg[iarg],"stop") == 0) break; if (strcmp(arg[iarg],"stop") == 0) break;
if (strcmp(arg[iarg],"dump") == 0) break; if (strcmp(arg[iarg],"dump") == 0) break;
if (strcmp(arg[iarg],"post") == 0) break;
iarg++; iarg++;
} }
int nfile = iarg; int nfile = iarg;
@ -65,6 +66,7 @@ void Rerun::command(int narg, char **arg)
int nskip = 1; int nskip = 1;
int startflag = 0; int startflag = 0;
int stopflag = 0; int stopflag = 0;
int postflag = 0;
bigint start = -1; bigint start = -1;
bigint stop = -1; bigint stop = -1;
@ -101,6 +103,14 @@ void Rerun::command(int narg, char **arg)
stop = utils::bnumeric(FLERR,arg[iarg+1],false,lmp); stop = utils::bnumeric(FLERR,arg[iarg+1],false,lmp);
if (stop < 0) error->all(FLERR,"Illegal rerun command"); if (stop < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"post") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
if (strcmp(arg[iarg+1],"yes") == 0) {
postflag = 1;
} else if (strcmp(arg[iarg+1],"no") == 0) {
postflag = 0;
} else error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"dump") == 0) { } else if (strcmp(arg[iarg],"dump") == 0) {
break; break;
} else error->all(FLERR,"Illegal rerun command"); } else error->all(FLERR,"Illegal rerun command");
@ -182,7 +192,7 @@ void Rerun::command(int narg, char **arg)
update->nsteps = ndump; update->nsteps = ndump;
Finish finish(lmp); Finish finish(lmp);
finish.end(1); finish.end(postflag);
update->whichflag = 0; update->whichflag = 0;
update->firststep = update->laststep = 0; update->firststep = update->laststep = 0;

4
src/tokenizer.h
View File

@ -41,7 +41,7 @@ public:
Tokenizer& operator=(Tokenizer&&) = default; Tokenizer& operator=(Tokenizer&&) = default;
void reset(); void reset();
void skip(int n); void skip(int n=1);
bool has_next() const; bool has_next() const;
bool contains(const std::string &str) const; bool contains(const std::string &str) const;
std::string next(); std::string next();
@ -104,7 +104,7 @@ public:
bool has_next() const; bool has_next() const;
bool contains(const std::string &value) const; bool contains(const std::string &value) const;
void skip(int ntokens); void skip(int ntokens=1);
size_t count(); size_t count();
}; };

2
src/velocity.cpp
View File

@ -108,7 +108,7 @@ void Velocity::command(int narg, char **arg)
int initcomm = 0; int initcomm = 0;
if (style == ZERO && rfix >= 0 && if (style == ZERO && rfix >= 0 &&
utils::strmatch(modify->fix[rfix]->style,"^rigid/small")) initcomm = 1; utils::strmatch(modify->fix[rfix]->style,"^rigid.*/small.*")) initcomm = 1;
if ((style == CREATE || style == SET) && temperature && if ((style == CREATE || style == SET) && temperature &&
strcmp(temperature->style,"temp/cs") == 0) initcomm = 1; strcmp(temperature->style,"temp/cs") == 0) initcomm = 1;

2
tools/singularity/ubuntu18.04_amd_rocm.def
View File

@ -94,7 +94,7 @@ From: ubuntu:18.04
########################################################################### ###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build mkdir hipCUB/build
cd hipCUB/build cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off .. CXX=hipcc cmake -D BUILD_TEST=off ..

4
tools/singularity/ubuntu20.04_amd_rocm.def
View File

@ -2,7 +2,7 @@ BootStrap: docker
From: ubuntu:20.04 From: ubuntu:20.04
%environment %environment
export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
%post %post
export DEBIAN_FRONTEND=noninteractive export DEBIAN_FRONTEND=noninteractive
apt-get update apt-get update
@ -90,7 +90,7 @@ From: ubuntu:20.04
########################################################################### ###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build mkdir hipCUB/build
cd hipCUB/build cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off .. CXX=hipcc cmake -D BUILD_TEST=off ..

4
unittest/commands/test_simple_commands.cpp
View File

@ -328,11 +328,7 @@ TEST_F(SimpleCommandsTest, Units)
#if defined(LMP_PLUGIN) #if defined(LMP_PLUGIN)
TEST_F(SimpleCommandsTest, Plugin) TEST_F(SimpleCommandsTest, Plugin)
{ {
#if defined(__APPLE__)
std::string loadfmt("plugin load {}plugin.dylib");
#else
std::string loadfmt("plugin load {}plugin.so"); std::string loadfmt("plugin load {}plugin.so");
#endif
::testing::internal::CaptureStdout(); ::testing::internal::CaptureStdout();
lmp->input->one(fmt::format(loadfmt, "hello")); lmp->input->one(fmt::format(loadfmt, "hello"));
auto text = ::testing::internal::GetCapturedStdout(); auto text = ::testing::internal::GetCapturedStdout();

2
unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
View File

@ -1,7 +1,7 @@
--- ---
lammps_version: 10 Mar 2021 lammps_version: 10 Mar 2021
date_generated: Thu Mar 25 14:07:45 202 date_generated: Thu Mar 25 14:07:45 202
epsilon: 1e-14 epsilon: 5e-13
prerequisites: ! | prerequisites: ! |
atom full atom full
fix adapt fix adapt

50
unittest/formats/test_dump_atom.cpp
View File

@ -15,6 +15,8 @@
#include "../testing/systems/melt.h" #include "../testing/systems/melt.h"
#include "../testing/utils.h" #include "../testing/utils.h"
#include "fmt/format.h" #include "fmt/format.h"
#include "output.h"
#include "thermo.h"
#include "utils.h" #include "utils.h"
#include "gmock/gmock.h" #include "gmock/gmock.h"
#include "gtest/gtest.h" #include "gtest/gtest.h"
@ -24,7 +26,7 @@
using ::testing::Eq; using ::testing::Eq;
char *BINARY2TXT_BINARY = nullptr; char *BINARY2TXT_BINARY = nullptr;
bool verbose = false; bool verbose = false;
class DumpAtomTest : public MeltTest { class DumpAtomTest : public MeltTest {
std::string dump_style = "atom"; std::string dump_style = "atom";
@ -46,7 +48,14 @@ public:
command(fmt::format("dump_modify id {}", dump_modify_options)); command(fmt::format("dump_modify id {}", dump_modify_options));
} }
command(fmt::format("run {}", ntimesteps)); command(fmt::format("run {} post no", ntimesteps));
END_HIDE_OUTPUT();
}
void continue_dump(int ntimesteps)
{
BEGIN_HIDE_OUTPUT();
command(fmt::format("run {} pre no post no", ntimesteps));
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
} }
@ -62,7 +71,7 @@ public:
command(fmt::format("dump_modify id1 {}", dump_modify_options)); command(fmt::format("dump_modify id1 {}", dump_modify_options));
} }
command(fmt::format("run {}", ntimesteps)); command(fmt::format("run {} post no", ntimesteps));
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
} }
@ -446,13 +455,16 @@ TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
delete_file(converted_file); delete_file(converted_file);
} }
TEST_F(DumpAtomTest, run1) TEST_F(DumpAtomTest, run1plus1)
{ {
auto dump_file = "dump_run1.melt"; auto dump_file = "dump_run1plus1.melt";
generate_dump(dump_file, "", 1); generate_dump(dump_file, "", 1);
ASSERT_FILE_EXISTS(dump_file); ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82); ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
delete_file(dump_file); delete_file(dump_file);
} }
@ -466,6 +478,34 @@ TEST_F(DumpAtomTest, run2)
delete_file(dump_file); delete_file(dump_file);
} }
TEST_F(DumpAtomTest, rerun)
{
auto dump_file = "dump_rerun.melt";
HIDE_OUTPUT([&] {
command("fix 1 all nve");
});
generate_dump(dump_file, "format line \"%d %d %20.15g %20.15g %20.15g\"", 1);
double pe_1, pe_2, pe_rerun;
lmp->output->thermo->evaluate_keyword("pe", &pe_1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_2, pe_rerun);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, multi_file_run1) TEST_F(DumpAtomTest, multi_file_run1)
{ {
auto dump_file = "dump_run1_*.melt"; auto dump_file = "dump_run1_*.melt";

73
unittest/formats/test_dump_custom.cpp
View File

@ -15,6 +15,8 @@
#include "../testing/systems/melt.h" #include "../testing/systems/melt.h"
#include "../testing/utils.h" #include "../testing/utils.h"
#include "fmt/format.h" #include "fmt/format.h"
#include "output.h"
#include "thermo.h"
#include "utils.h" #include "utils.h"
#include "gmock/gmock.h" #include "gmock/gmock.h"
#include "gtest/gtest.h" #include "gtest/gtest.h"
@ -22,7 +24,7 @@
using ::testing::Eq; using ::testing::Eq;
char *BINARY2TXT_BINARY = nullptr; char *BINARY2TXT_BINARY = nullptr;
bool verbose = false; bool verbose = false;
class DumpCustomTest : public MeltTest { class DumpCustomTest : public MeltTest {
std::string dump_style = "custom"; std::string dump_style = "custom";
@ -45,7 +47,14 @@ public:
command(fmt::format("dump_modify id {}", dump_modify_options)); command(fmt::format("dump_modify id {}", dump_modify_options));
} }
command(fmt::format("run {}", ntimesteps)); command(fmt::format("run {} post no", ntimesteps));
END_HIDE_OUTPUT();
}
void continue_dump(int ntimesteps)
{
BEGIN_HIDE_OUTPUT();
command(fmt::format("run {} pre no post no", ntimesteps));
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
} }
@ -62,7 +71,7 @@ public:
command(fmt::format("dump_modify id1 {}", dump_modify_options)); command(fmt::format("dump_modify id1 {}", dump_modify_options));
} }
command(fmt::format("run {}", ntimesteps)); command(fmt::format("run {} post no", ntimesteps));
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
} }
@ -262,6 +271,64 @@ TEST_F(DumpCustomTest, with_variable_run1)
delete_file(dump_file); delete_file(dump_file);
} }
TEST_F(DumpCustomTest, run1plus1)
{
auto dump_file = "dump_custom_run1plus1.melt";
auto fields = "id type x y z";
generate_dump(dump_file, fields, "units yes", 1);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 84);
continue_dump(1);
ASSERT_FILE_EXISTS(dump_file);
lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 125);
delete_file(dump_file);
}
TEST_F(DumpCustomTest, run2)
{
auto dump_file = "dump_custom_run2.melt";
auto fields = "id type x y z";
generate_dump(dump_file, fields, "", 2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
delete_file(dump_file);
}
TEST_F(DumpCustomTest, rerun)
{
auto dump_file = "dump_rerun.melt";
auto fields = "id type xs ys zs";
HIDE_OUTPUT([&] {
command("fix 1 all nve");
});
generate_dump(dump_file, fields, "format float %20.15g", 1);
double pe_1, pe_2, pe_rerun;
lmp->output->thermo->evaluate_keyword("pe", &pe_1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_2, pe_rerun);
delete_file(dump_file);
}
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
MPI_Init(&argc, &argv); MPI_Init(&argc, &argv);

62
unittest/formats/test_potential_file_reader.cpp
View File

@ -28,6 +28,7 @@
#include "potential_file_reader.h" #include "potential_file_reader.h"
#include "gmock/gmock.h" #include "gmock/gmock.h"
#include "gtest/gtest.h" #include "gtest/gtest.h"
#include "../testing/core.h" #include "../testing/core.h"
#include <cstring> #include <cstring>
@ -257,6 +258,67 @@ TEST_F(PotentialFileReaderTest, UnitConvert)
delete reader; delete reader;
} }
class OpenPotentialTest : public LAMMPSTest {
};
// open for native units
TEST_F(OpenPotentialTest, Sw_native)
{
int convert_flag = utils::get_supported_conversions(utils::ENERGY);
BEGIN_CAPTURE_OUTPUT();
command("units metal");
FILE *fp = utils::open_potential("Si.sw", lmp, &convert_flag);
auto text = END_CAPTURE_OUTPUT();
double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag);
ASSERT_NE(fp, nullptr);
ASSERT_DOUBLE_EQ(conv, 1.0);
fclose(fp);
}
// open with supported conversion enabled
TEST_F(OpenPotentialTest, Sw_conv)
{
int convert_flag = utils::get_supported_conversions(utils::ENERGY);
ASSERT_EQ(convert_flag, utils::METAL2REAL | utils::REAL2METAL);
BEGIN_HIDE_OUTPUT();
command("units real");
FILE *fp = utils::open_potential("Si.sw", lmp, &convert_flag);
auto text = END_CAPTURE_OUTPUT();
double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag);
ASSERT_NE(fp, nullptr);
ASSERT_EQ(convert_flag, utils::METAL2REAL);
ASSERT_DOUBLE_EQ(conv, 23.060549);
fclose(fp);
}
// open with conversion disabled
TEST_F(OpenPotentialTest, Sw_noconv)
{
BEGIN_HIDE_OUTPUT();
command("units real");
END_HIDE_OUTPUT();
TEST_FAILURE(".*potential.*requires metal units but real.*",
utils::open_potential("Si.sw", lmp, nullptr););
BEGIN_HIDE_OUTPUT();
command("units lj");
END_HIDE_OUTPUT();
int convert_flag = utils::get_supported_conversions(utils::UNKNOWN);
ASSERT_EQ(convert_flag, utils::NOCONVERT);
}
// open non-existing potential
TEST_F(OpenPotentialTest, No_file)
{
int convert_flag = utils::get_supported_conversions(utils::ENERGY);
BEGIN_HIDE_OUTPUT();
command("units metal");
FILE *fp = utils::open_potential("Unknown.sw", lmp, &convert_flag);
END_HIDE_OUTPUT();
ASSERT_EQ(fp,nullptr);
}
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
MPI_Init(&argc, &argv); MPI_Init(&argc, &argv);

44
unittest/utils/test_tokenizer.cpp
View File

@ -43,6 +43,18 @@ TEST(Tokenizer, two_words)
ASSERT_EQ(t.count(), 2); ASSERT_EQ(t.count(), 2);
} }
TEST(Tokenizer, skip)
{
Tokenizer t("test word", " ");
ASSERT_TRUE(t.has_next());
t.skip();
ASSERT_TRUE(t.has_next());
t.skip(1);
ASSERT_FALSE(t.has_next());
ASSERT_EQ(t.count(), 2);
ASSERT_THROW(t.skip(), TokenizerException);
}
TEST(Tokenizer, prefix_separators) TEST(Tokenizer, prefix_separators)
{ {
Tokenizer t(" test word", " "); Tokenizer t(" test word", " ");
@ -63,6 +75,18 @@ TEST(Tokenizer, iterate_words)
ASSERT_EQ(t.count(), 2); ASSERT_EQ(t.count(), 2);
} }
TEST(Tokenizer, copy_constructor)
{
Tokenizer t(" test word ", " ");
ASSERT_THAT(t.next(), Eq("test"));
ASSERT_THAT(t.next(), Eq("word"));
ASSERT_EQ(t.count(), 2);
Tokenizer u(t);
ASSERT_THAT(u.next(), Eq("test"));
ASSERT_THAT(u.next(), Eq("word"));
ASSERT_EQ(u.count(), 2);
}
TEST(Tokenizer, no_separator_path) TEST(Tokenizer, no_separator_path)
{ {
Tokenizer t("one", ":"); Tokenizer t("one", ":");
@ -139,6 +163,26 @@ TEST(ValueTokenizer, empty_string)
ASSERT_FALSE(values.has_next()); ASSERT_FALSE(values.has_next());
} }
TEST(ValueTokenizer, two_words)
{
ValueTokenizer t("test word", " ");
ASSERT_THAT(t.next_string(), Eq("test"));
ASSERT_THAT(t.next_string(), Eq("word"));
ASSERT_THROW(t.next_string(), TokenizerException);
}
TEST(ValueTokenizer, skip)
{
ValueTokenizer t("test word", " ");
ASSERT_TRUE(t.has_next());
t.skip();
ASSERT_TRUE(t.has_next());
t.skip(1);
ASSERT_FALSE(t.has_next());
ASSERT_EQ(t.count(), 2);
ASSERT_THROW(t.skip(), TokenizerException);
}
TEST(ValueTokenizer, bad_integer) TEST(ValueTokenizer, bad_integer)
{ {
ValueTokenizer values("f10"); ValueTokenizer values("f10");

44
unittest/utils/test_utils.cpp
View File

@ -331,6 +331,11 @@ TEST(Utils, valid_id7)
ASSERT_TRUE(utils::is_id("___")); ASSERT_TRUE(utils::is_id("___"));
} }
TEST(Utils, empty_id)
{
ASSERT_FALSE(utils::is_id(""));
}
TEST(Utils, invalid_id1) TEST(Utils, invalid_id1)
{ {
ASSERT_FALSE(utils::is_id("+abc")); ASSERT_FALSE(utils::is_id("+abc"));
@ -780,6 +785,11 @@ TEST(Utils, unit_conversion)
ASSERT_DOUBLE_EQ(factor, 1.0 / 23.060549); ASSERT_DOUBLE_EQ(factor, 1.0 / 23.060549);
} }
TEST(Utils, timespec2seconds_off)
{
ASSERT_DOUBLE_EQ(utils::timespec2seconds("off"), -1.0);
}
TEST(Utils, timespec2seconds_ss) TEST(Utils, timespec2seconds_ss)
{ {
ASSERT_DOUBLE_EQ(utils::timespec2seconds("45"), 45.0); ASSERT_DOUBLE_EQ(utils::timespec2seconds("45"), 45.0);
@ -795,6 +805,11 @@ TEST(Utils, timespec2seconds_hhmmss)
ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0); ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0);
} }
TEST(Utils, timespec2seconds_invalid)
{
ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:aa:45"), -1.0);
}
TEST(Utils, date2num) TEST(Utils, date2num)
{ {
ASSERT_EQ(utils::date2num("1Jan05"), 20050101); ASSERT_EQ(utils::date2num("1Jan05"), 20050101);
@ -810,3 +825,32 @@ TEST(Utils, date2num)
ASSERT_EQ(utils::date2num("30November 02"), 20021130); ASSERT_EQ(utils::date2num("30November 02"), 20021130);
ASSERT_EQ(utils::date2num("31December100"), 1001231); ASSERT_EQ(utils::date2num("31December100"), 1001231);
} }
static int compare(int a, int b, void *)
{
if (a < b)
return -1;
else if (a > b)
return 1;
else
return 0;
}
TEST(Utils, merge_sort)
{
int data[] = {773, 405, 490, 830, 632, 96, 428, 728, 912, 840, 878, 745, 213, 219, 249, 380,
894, 758, 575, 690, 61, 849, 19, 577, 338, 569, 898, 873, 448, 940, 431, 780,
472, 289, 65, 491, 641, 37, 367, 33, 407, 854, 594, 611, 845, 136, 107, 592,
275, 865, 158, 626, 399, 703, 686, 734, 188, 559, 781, 558, 737, 281, 638, 664,
533, 529, 62, 969, 595, 661, 837, 463, 624, 568, 615, 936, 206, 637, 91, 694,
214, 872, 468, 66, 775, 949, 486, 576, 255, 961, 480, 138, 177, 509, 333, 705,
10, 375, 321, 952, 210, 111, 475, 268, 708, 864, 244, 121, 988, 540, 942, 682,
750, 473, 478, 714, 955, 911, 482, 384, 144, 757, 697, 791, 420, 605, 447, 320};
const int num = sizeof(data) / sizeof(int);
utils::merge_sort(data, num, nullptr, &compare);
bool sorted = true;
for (int i = 1; i < num; ++i)
if (data[i - 1] > data[i]) sorted = false;
ASSERT_TRUE(sorted);
}