Merge branch 'master' into feature/user-pace
This commit is contained in:
Axel Kohlmeyer
4
.github/workflows/unittest-macos.yml
vendored
4
.github/workflows/unittest-macos.yml
vendored
@ -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
|
||||||
|
|
||||||
|
|||||||
@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools)
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|||||||
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
|
||||||
|
|||||||
@ -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)
|
||||||
|
|||||||
@ -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} ${CMAKE_EXTRA_GTEST_OPTS}
|
||||||
|
|||||||
@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
|
|||||||
# fetch missing potential files
|
# fetch missing potential files
|
||||||
function(FetchPotentials pkgfolder potfolder)
|
function(FetchPotentials pkgfolder potfolder)
|
||||||
if (EXISTS "${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 ${line} " " blank)
|
||||||
|
|||||||
@ -1,16 +1,25 @@
|
|||||||
# Download and configure custom MPICH files for Windows
|
# Download and configure custom MPICH files for Windows
|
||||||
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
|
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
|
||||||
|
set(MPICH2_WIN64_DEVEL_URL "${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 ${MPICH2_WIN32_DEVEL_MD5}
|
||||||
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
|
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
|
||||||
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
|
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -1,11 +1,13 @@
|
|||||||
message(STATUS "Downloading and building OpenCL loader library")
|
message(STATUS "Downloading and building OpenCL loader library")
|
||||||
|
set(OPENCL_LOADER_URL "${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}
|
||||||
|
|||||||
@ -131,7 +131,7 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
|
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
|
||||||
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||||
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
|
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
|
||||||
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
|
target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
|
||||||
if(CUDPP_OPT)
|
if(CUDPP_OPT)
|
||||||
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
||||||
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
|
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
|
||||||
@ -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)
|
||||||
|
|||||||
@ -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=${CMAKE_C_COMPILER}
|
||||||
|
|||||||
@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${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
|
||||||
)
|
)
|
||||||
|
|||||||
@ -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}
|
||||||
|
|||||||
@ -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}
|
||||||
|
|||||||
@ -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}
|
||||||
|
|||||||
@ -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
|
||||||
|
|||||||
@ -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)
|
||||||
|
|||||||
@ -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}
|
||||||
|
|||||||
@ -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}
|
||||||
|
|||||||
@ -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)
|
||||||
|
|||||||
@ -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>`
|
||||||
|
|||||||
@ -76,7 +76,7 @@ It documents the following functions:
|
|||||||
|
|
||||||
-----------------------
|
-----------------------
|
||||||
|
|
||||||
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand)
|
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
|
||||||
:project: progguide
|
:project: progguide
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -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 |
|
||||||
|
|||||||
@ -142,7 +142,7 @@ Style Constants
|
|||||||
Type Constants
|
Type Constants
|
||||||
--------------
|
--------------
|
||||||
|
|
||||||
.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
|
.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
|
||||||
:type: int
|
:type: int
|
||||||
|
|
||||||
Constants in the :py:mod:`lammps` module to select what type of data
|
Constants in the :py:mod:`lammps` module to select what type of data
|
||||||
|
|||||||
@ -1,6 +1,43 @@
|
|||||||
Neighbor list access
|
Neighbor list access
|
||||||
====================
|
====================
|
||||||
|
|
||||||
|
Access to neighbor lists is handled through a couple of wrapper classes
|
||||||
|
that allows to treat it like either a python list or a NumPy array. The
|
||||||
|
access procedure is similar to that of the C-library interface: use one
|
||||||
|
of the "find" functions to look up the index of the neighbor list in the
|
||||||
|
global table of neighbor lists and then get access to the neighbor list
|
||||||
|
data. The code sample below demonstrates reading the neighbor list data
|
||||||
|
using the NumPy access method.
|
||||||
|
|
||||||
|
.. code-block:: python
|
||||||
|
|
||||||
|
from lammps import lammps
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
lmp = lammps()
|
||||||
|
lmp.commands_string("""
|
||||||
|
region box block -2 2 -2 2 -2 2
|
||||||
|
lattice fcc 1.0
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass 1 1.0
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0
|
||||||
|
run 0 post no""")
|
||||||
|
|
||||||
|
# look up the neighbor list
|
||||||
|
nlidx = lmp.find_pair_neighlist('lj/cut')
|
||||||
|
nl = lmp.numpy.get_neighlist(nlidx)
|
||||||
|
tags = lmp.extract_atom('id')
|
||||||
|
print("half neighbor list with {} entries".format(nl.size))
|
||||||
|
# print neighbor list contents
|
||||||
|
for i in range(0,nl.size):
|
||||||
|
idx, nlist = nl.get(i)
|
||||||
|
print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
|
||||||
|
if nlist.size > 0:
|
||||||
|
for n in np.nditer(nlist):
|
||||||
|
print(" atom {} with ID {}".format(n,tags[n]))
|
||||||
|
|
||||||
**Methods:**
|
**Methods:**
|
||||||
|
|
||||||
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index
|
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index
|
||||||
|
|||||||
@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one. E.g. these
|
|||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
compute myCOM all com/chunk
|
compute myCOM all com/chunk
|
||||||
fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
|
fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
|
||||||
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
|
fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
|
||||||
|
|
||||||
If the fix ave/histo/weight command is used, exactly two values must
|
If the fix ave/histo/weight command is used, exactly two values must
|
||||||
be specified. If the values are vectors, they must be the same
|
be specified. If the values are vectors, they must be the same
|
||||||
|
|||||||
@ -29,6 +29,7 @@ Syntax
|
|||||||
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
|
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
|
||||||
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
|
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
|
||||||
dampflag = 0 or 1 if tangential damping force is excluded or included
|
dampflag = 0 or 1 if tangential damping force is excluded or included
|
||||||
|
optional keyword = *limit_damping*, limit damping to prevent attractive interaction
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -95,7 +96,8 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff
|
|||||||
= mass of particle, and the effective radius of contact = RiRj/Ri+Rj is
|
= mass of particle, and the effective radius of contact = RiRj/Ri+Rj is
|
||||||
set to the radius of the particle.
|
set to the radius of the particle.
|
||||||
|
|
||||||
The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag*
|
The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*,
|
||||||
|
and the optional keyword *limit_damping*
|
||||||
have the same meaning and units as those specified with the
|
have the same meaning and units as those specified with the
|
||||||
:doc:`pair_style gran/\* <pair_gran>` commands. This means a NULL can be
|
:doc:`pair_style gran/\* <pair_gran>` commands. This means a NULL can be
|
||||||
used for either *Kt* or *gamma_t* as described on that page. If a
|
used for either *Kt* or *gamma_t* as described on that page. If a
|
||||||
|
|||||||
@ -181,7 +181,8 @@ radius - r = overlap of particle with wall, m_eff = mass of particle,
|
|||||||
and the effective radius of contact is just the radius of the
|
and the effective radius of contact is just the radius of the
|
||||||
particle.
|
particle.
|
||||||
|
|
||||||
The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag*
|
The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*,
|
||||||
|
and the optional keyword *limit_damping*
|
||||||
have the same meaning and units as those specified with the
|
have the same meaning and units as those specified with the
|
||||||
:doc:`pair_style gran/\* <pair_gran>` commands. This means a NULL can be
|
:doc:`pair_style gran/\* <pair_gran>` commands. This means a NULL can be
|
||||||
used for either *Kt* or *gamma_t* as described on that page. If a
|
used for either *Kt* or *gamma_t* as described on that page. If a
|
||||||
|
|||||||
@ -26,7 +26,7 @@ Syntax
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
pair_style style Kn Kt gamma_n gamma_t xmu dampflag
|
pair_style style Kn Kt gamma_n gamma_t xmu dampflag keyword
|
||||||
|
|
||||||
* style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history*
|
* style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history*
|
||||||
* Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
|
* Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
|
||||||
@ -36,6 +36,13 @@ Syntax
|
|||||||
* xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
|
* xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
|
||||||
* dampflag = 0 or 1 if tangential damping force is excluded or included
|
* dampflag = 0 or 1 if tangential damping force is excluded or included
|
||||||
|
|
||||||
|
* keyword = *limit_damping*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
*limit_damping* value = none
|
||||||
|
limit damping to prevent attractive interaction
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
Versions of LAMMPS before 9Jan09 had different style names for
|
Versions of LAMMPS before 9Jan09 had different style names for
|
||||||
@ -54,6 +61,8 @@ Examples
|
|||||||
|
|
||||||
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
|
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
|
||||||
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
|
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
|
||||||
|
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 limit_damping
|
||||||
|
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -208,6 +217,12 @@ potential is used as a sub-style of :doc:`pair_style hybrid <pair_hybrid>`, then
|
|||||||
pair_coeff command to determine which atoms interact via a granular
|
pair_coeff command to determine which atoms interact via a granular
|
||||||
potential.
|
potential.
|
||||||
|
|
||||||
|
If two particles are moving away from each other while in contact, there
|
||||||
|
is a possibility that the particles could experience an effective attractive
|
||||||
|
force due to damping. If the *limit_damping* keyword is used, this option
|
||||||
|
will zero out the normal component of the force if there is an effective
|
||||||
|
attractive force.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. include:: accel_styles.rst
|
.. include:: accel_styles.rst
|
||||||
|
|||||||
@ -24,7 +24,7 @@ Examples
|
|||||||
pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
|
pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
|
||||||
|
|
||||||
pair_style granular
|
pair_style granular
|
||||||
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4
|
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 limit_damping
|
||||||
|
|
||||||
pair_style granular
|
pair_style granular
|
||||||
pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
|
pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
|
||||||
@ -623,6 +623,14 @@ Finally, the twisting torque on each particle is given by:
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
If two particles are moving away from each other while in contact, there
|
||||||
|
is a possibility that the particles could experience an effective attractive
|
||||||
|
force due to damping. If the optional *limit_damping* keyword is used, this option
|
||||||
|
will zero out the normal component of the force if there is an effective
|
||||||
|
attractive force. This keyword cannot be used with the JKR or DMT models.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
The *granular* pair style can reproduce the behavior of the
|
The *granular* pair style can reproduce the behavior of the
|
||||||
*pair gran/\** styles with the appropriate settings (some very
|
*pair gran/\** styles with the appropriate settings (some very
|
||||||
minor differences can be expected due to corrections in
|
minor differences can be expected due to corrections in
|
||||||
@ -657,6 +665,12 @@ then LAMMPS will use that cutoff for the specified atom type
|
|||||||
combination, and automatically set pairwise cutoffs for the remaining
|
combination, and automatically set pairwise cutoffs for the remaining
|
||||||
atom types.
|
atom types.
|
||||||
|
|
||||||
|
If two particles are moving away from each other while in contact, there
|
||||||
|
is a possibility that the particles could experience an effective attractive
|
||||||
|
force due to damping. If the *limit_damping* keyword is used, this option
|
||||||
|
will zero out the normal component of the force if there is an effective
|
||||||
|
attractive force. This keyword cannot be used with the JKR or DMT models.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. include:: accel_styles.rst
|
.. include:: accel_styles.rst
|
||||||
|
|||||||
@ -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;
|
||||||
|
|||||||
@ -2693,6 +2693,7 @@ representable
|
|||||||
Reproducibility
|
Reproducibility
|
||||||
reproducibility
|
reproducibility
|
||||||
repuls
|
repuls
|
||||||
|
reqid
|
||||||
rescale
|
rescale
|
||||||
rescaled
|
rescaled
|
||||||
rescales
|
rescales
|
||||||
|
|||||||
56
examples/deposit/in.deposit.molecule.rigid-nve-small
Normal file
56
examples/deposit/in.deposit.molecule.rigid-nve-small
Normal file
@ -0,0 +1,56 @@
|
|||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nve/small molecule mol dimer
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
|
||||||
|
mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type &
|
||||||
|
# axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type &
|
||||||
|
# axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
56
examples/deposit/in.deposit.molecule.rigid-nvt-small
Normal file
56
examples/deposit/in.deposit.molecule.rigid-nvt-small
Normal file
@ -0,0 +1,56 @@
|
|||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
|
||||||
|
mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type &
|
||||||
|
# axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type &
|
||||||
|
# axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
@ -0,0 +1,218 @@
|
|||||||
|
LAMMPS (10 Mar 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
Created 350 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
Read molecule template dimer:
|
||||||
|
1 molecules
|
||||||
|
2 atoms with max type 3
|
||||||
|
1 bonds with max type 1
|
||||||
|
0 angles with max type 0
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
0 atoms in group addatoms
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
150 atoms in group mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nve/small molecule mol dimer
|
||||||
|
create bodies CPU = 0.000 seconds
|
||||||
|
0 rigid bodies with 0 atoms
|
||||||
|
1.0000000 = max distance from body owner to body atom
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.3
|
||||||
|
ghost atom cutoff = 5.3
|
||||||
|
binsize = 2.65, bins = 3 3 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
|
||||||
|
Step Atoms Temp E_pair TotEng Press
|
||||||
|
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||||
|
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
|
||||||
|
200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
|
||||||
|
300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
|
||||||
|
400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
|
||||||
|
500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
|
||||||
|
600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
|
||||||
|
700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
|
||||||
|
800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615
|
||||||
|
900 368 1.1250034 -6.6101882 -6.541404 -0.66674346
|
||||||
|
1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655
|
||||||
|
1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041
|
||||||
|
1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272
|
||||||
|
1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641
|
||||||
|
1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595
|
||||||
|
1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503
|
||||||
|
1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922
|
||||||
|
1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709
|
||||||
|
1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665
|
||||||
|
1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025
|
||||||
|
2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647
|
||||||
|
2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526
|
||||||
|
2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284
|
||||||
|
2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436
|
||||||
|
2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839
|
||||||
|
2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448
|
||||||
|
2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222
|
||||||
|
2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856
|
||||||
|
2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872
|
||||||
|
2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283
|
||||||
|
3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953
|
||||||
|
3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935
|
||||||
|
3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713
|
||||||
|
3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674
|
||||||
|
3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626
|
||||||
|
3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941
|
||||||
|
3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484
|
||||||
|
3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147
|
||||||
|
3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799
|
||||||
|
3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878
|
||||||
|
4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433
|
||||||
|
4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822
|
||||||
|
4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778
|
||||||
|
4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913
|
||||||
|
4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275
|
||||||
|
4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051
|
||||||
|
4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572
|
||||||
|
4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509
|
||||||
|
4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049
|
||||||
|
4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429
|
||||||
|
5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531
|
||||||
|
5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403
|
||||||
|
5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239
|
||||||
|
5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702
|
||||||
|
5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883
|
||||||
|
5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171
|
||||||
|
5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419
|
||||||
|
5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563
|
||||||
|
5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625
|
||||||
|
5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757
|
||||||
|
6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047
|
||||||
|
6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913
|
||||||
|
6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083
|
||||||
|
6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967
|
||||||
|
6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489
|
||||||
|
6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516
|
||||||
|
6600 482 0.354106 -6.6890268 -6.567808 -0.81897158
|
||||||
|
6700 484 0.3504816 -6.681739 -6.5604463 -0.811609
|
||||||
|
6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296
|
||||||
|
6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651
|
||||||
|
7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078
|
||||||
|
7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001
|
||||||
|
7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767
|
||||||
|
7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121
|
||||||
|
7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584
|
||||||
|
7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602
|
||||||
|
7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497
|
||||||
|
7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548
|
||||||
|
7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084
|
||||||
|
7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684
|
||||||
|
8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575
|
||||||
|
8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457
|
||||||
|
8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287
|
||||||
|
8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937
|
||||||
|
8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496
|
||||||
|
8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738
|
||||||
|
8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327
|
||||||
|
8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016
|
||||||
|
8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456
|
||||||
|
8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919
|
||||||
|
9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061
|
||||||
|
9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298
|
||||||
|
9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671
|
||||||
|
9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602
|
||||||
|
9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131
|
||||||
|
9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326
|
||||||
|
9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105
|
||||||
|
9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932
|
||||||
|
9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759
|
||||||
|
9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312
|
||||||
|
10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213
|
||||||
|
Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms
|
||||||
|
|
||||||
|
Performance: 258256.688 tau/day, 597.816 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.2508 | 9.2508 | 9.2508 | 0.0 | 55.30
|
||||||
|
Bond | 0.021603 | 0.021603 | 0.021603 | 0.0 | 0.13
|
||||||
|
Neigh | 4.5325 | 4.5325 | 4.5325 | 0.0 | 27.10
|
||||||
|
Comm | 0.62777 | 0.62777 | 0.62777 | 0.0 | 3.75
|
||||||
|
Output | 0.006916 | 0.006916 | 0.006916 | 0.0 | 0.04
|
||||||
|
Modify | 2.218 | 2.218 | 2.218 | 0.0 | 13.26
|
||||||
|
Other | | 0.07002 | | | 0.42
|
||||||
|
|
||||||
|
Nlocal: 550.000 ave 550 max 550 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2344.00 ave 2344 max 2344 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 36607.0 ave 36607 max 36607 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 36607
|
||||||
|
Ave neighs/atom = 66.558182
|
||||||
|
Ave special neighs/atom = 0.36363636
|
||||||
|
Neighbor list builds = 847
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:16
|
||||||
@ -0,0 +1,218 @@
|
|||||||
|
LAMMPS (10 Mar 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||||
|
1 by 1 by 4 MPI processor grid
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
Created 350 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
Read molecule template dimer:
|
||||||
|
1 molecules
|
||||||
|
2 atoms with max type 3
|
||||||
|
1 bonds with max type 1
|
||||||
|
0 angles with max type 0
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
0 atoms in group addatoms
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
150 atoms in group mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nve/small molecule mol dimer
|
||||||
|
create bodies CPU = 0.000 seconds
|
||||||
|
0 rigid bodies with 0 atoms
|
||||||
|
1.0000000 = max distance from body owner to body atom
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.3
|
||||||
|
ghost atom cutoff = 5.3
|
||||||
|
binsize = 2.65, bins = 3 3 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
||||||
|
Step Atoms Temp E_pair TotEng Press
|
||||||
|
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||||
|
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
||||||
|
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
||||||
|
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
||||||
|
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
||||||
|
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
||||||
|
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
||||||
|
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
||||||
|
800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282
|
||||||
|
900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928
|
||||||
|
1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047
|
||||||
|
1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289
|
||||||
|
1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821
|
||||||
|
1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688
|
||||||
|
1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401
|
||||||
|
1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986
|
||||||
|
1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779
|
||||||
|
1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111
|
||||||
|
1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786
|
||||||
|
1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098
|
||||||
|
2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072
|
||||||
|
2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411
|
||||||
|
2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854
|
||||||
|
2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918
|
||||||
|
2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214
|
||||||
|
2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183
|
||||||
|
2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893
|
||||||
|
2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506
|
||||||
|
2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082
|
||||||
|
2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652
|
||||||
|
3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355
|
||||||
|
3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541
|
||||||
|
3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248
|
||||||
|
3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819
|
||||||
|
3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309
|
||||||
|
3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397
|
||||||
|
3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391
|
||||||
|
3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397
|
||||||
|
3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111
|
||||||
|
3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465
|
||||||
|
4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933
|
||||||
|
4100 432 0.44820466 -6.640222 -6.5338771 -0.805972
|
||||||
|
4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414
|
||||||
|
4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484
|
||||||
|
4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062
|
||||||
|
4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194
|
||||||
|
4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114
|
||||||
|
4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577
|
||||||
|
4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746
|
||||||
|
4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416
|
||||||
|
5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399
|
||||||
|
5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755
|
||||||
|
5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092
|
||||||
|
5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134
|
||||||
|
5400 458 0.37764326 -6.661431 -6.550117 -0.72187808
|
||||||
|
5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745
|
||||||
|
5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454
|
||||||
|
5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312
|
||||||
|
5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125
|
||||||
|
5900 468 0.346812 -6.681215 -6.57191 -0.81184233
|
||||||
|
6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821
|
||||||
|
6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598
|
||||||
|
6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526
|
||||||
|
6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174
|
||||||
|
6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407
|
||||||
|
6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289
|
||||||
|
6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442
|
||||||
|
6700 484 0.37615026 -6.722917 -6.592741 -0.76534055
|
||||||
|
6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211
|
||||||
|
6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458
|
||||||
|
7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555
|
||||||
|
7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708
|
||||||
|
7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153
|
||||||
|
7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931
|
||||||
|
7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391
|
||||||
|
7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083
|
||||||
|
7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572
|
||||||
|
7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335
|
||||||
|
7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197
|
||||||
|
7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073
|
||||||
|
8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575
|
||||||
|
8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257
|
||||||
|
8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132
|
||||||
|
8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415
|
||||||
|
8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921
|
||||||
|
8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077
|
||||||
|
8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137
|
||||||
|
8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836
|
||||||
|
8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107
|
||||||
|
8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959
|
||||||
|
9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529
|
||||||
|
9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692
|
||||||
|
9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911
|
||||||
|
9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935
|
||||||
|
9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598
|
||||||
|
9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851
|
||||||
|
9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104
|
||||||
|
9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581
|
||||||
|
9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905
|
||||||
|
9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157
|
||||||
|
10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157
|
||||||
|
Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms
|
||||||
|
|
||||||
|
Performance: 265759.101 tau/day, 615.183 timesteps/s
|
||||||
|
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0034051 | 2.6646 | 8.0317 | 200.7 | 16.39
|
||||||
|
Bond | 0.0022626 | 0.0072971 | 0.019437 | 8.3 | 0.04
|
||||||
|
Neigh | 0.018657 | 1.218 | 3.7621 | 137.5 | 7.49
|
||||||
|
Comm | 1.1497 | 6.7957 | 12.192 | 164.2 | 41.81
|
||||||
|
Output | 0.010692 | 0.01431 | 0.019901 | 3.2 | 0.09
|
||||||
|
Modify | 3.1502 | 5.3779 | 11.342 | 149.0 | 33.08
|
||||||
|
Other | | 0.1775 | | | 1.09
|
||||||
|
|
||||||
|
Nlocal: 137.500 ave 299 max 2 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 1903.75 ave 2686 max 529 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||||
|
Neighs: 9209.75 ave 23206 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 36839
|
||||||
|
Ave neighs/atom = 66.980000
|
||||||
|
Ave special neighs/atom = 0.36363636
|
||||||
|
Neighbor list builds = 829
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:16
|
||||||
@ -0,0 +1,218 @@
|
|||||||
|
LAMMPS (10 Mar 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
Created 350 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
Read molecule template dimer:
|
||||||
|
1 molecules
|
||||||
|
2 atoms with max type 3
|
||||||
|
1 bonds with max type 1
|
||||||
|
0 angles with max type 0
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
0 atoms in group addatoms
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
150 atoms in group mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
|
||||||
|
create bodies CPU = 0.000 seconds
|
||||||
|
0 rigid bodies with 0 atoms
|
||||||
|
1.0000000 = max distance from body owner to body atom
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.3
|
||||||
|
ghost atom cutoff = 5.3
|
||||||
|
binsize = 2.65, bins = 3 3 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
|
||||||
|
Step Atoms Temp E_pair TotEng Press
|
||||||
|
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||||
|
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
|
||||||
|
200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
|
||||||
|
300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
|
||||||
|
400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
|
||||||
|
500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
|
||||||
|
600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
|
||||||
|
700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
|
||||||
|
800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615
|
||||||
|
900 368 1.1250034 -6.6101882 -6.541404 -0.66674346
|
||||||
|
1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655
|
||||||
|
1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041
|
||||||
|
1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272
|
||||||
|
1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641
|
||||||
|
1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595
|
||||||
|
1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503
|
||||||
|
1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922
|
||||||
|
1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709
|
||||||
|
1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665
|
||||||
|
1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025
|
||||||
|
2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647
|
||||||
|
2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526
|
||||||
|
2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284
|
||||||
|
2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436
|
||||||
|
2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839
|
||||||
|
2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448
|
||||||
|
2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222
|
||||||
|
2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856
|
||||||
|
2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872
|
||||||
|
2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283
|
||||||
|
3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953
|
||||||
|
3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935
|
||||||
|
3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713
|
||||||
|
3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674
|
||||||
|
3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626
|
||||||
|
3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941
|
||||||
|
3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484
|
||||||
|
3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147
|
||||||
|
3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799
|
||||||
|
3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878
|
||||||
|
4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433
|
||||||
|
4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822
|
||||||
|
4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778
|
||||||
|
4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913
|
||||||
|
4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275
|
||||||
|
4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051
|
||||||
|
4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572
|
||||||
|
4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509
|
||||||
|
4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049
|
||||||
|
4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429
|
||||||
|
5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531
|
||||||
|
5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403
|
||||||
|
5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239
|
||||||
|
5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702
|
||||||
|
5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883
|
||||||
|
5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171
|
||||||
|
5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419
|
||||||
|
5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563
|
||||||
|
5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625
|
||||||
|
5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757
|
||||||
|
6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047
|
||||||
|
6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913
|
||||||
|
6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083
|
||||||
|
6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967
|
||||||
|
6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489
|
||||||
|
6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516
|
||||||
|
6600 482 0.354106 -6.6890268 -6.567808 -0.81897158
|
||||||
|
6700 484 0.3504816 -6.681739 -6.5604463 -0.811609
|
||||||
|
6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296
|
||||||
|
6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651
|
||||||
|
7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078
|
||||||
|
7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001
|
||||||
|
7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767
|
||||||
|
7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121
|
||||||
|
7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584
|
||||||
|
7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602
|
||||||
|
7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497
|
||||||
|
7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548
|
||||||
|
7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084
|
||||||
|
7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684
|
||||||
|
8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575
|
||||||
|
8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457
|
||||||
|
8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287
|
||||||
|
8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937
|
||||||
|
8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496
|
||||||
|
8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738
|
||||||
|
8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327
|
||||||
|
8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016
|
||||||
|
8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456
|
||||||
|
8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919
|
||||||
|
9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061
|
||||||
|
9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298
|
||||||
|
9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671
|
||||||
|
9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602
|
||||||
|
9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131
|
||||||
|
9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326
|
||||||
|
9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105
|
||||||
|
9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932
|
||||||
|
9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759
|
||||||
|
9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312
|
||||||
|
10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213
|
||||||
|
Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms
|
||||||
|
|
||||||
|
Performance: 259279.806 tau/day, 600.185 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60
|
||||||
|
Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13
|
||||||
|
Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27
|
||||||
|
Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77
|
||||||
|
Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04
|
||||||
|
Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77
|
||||||
|
Other | | 0.06897 | | | 0.41
|
||||||
|
|
||||||
|
Nlocal: 550.000 ave 550 max 550 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2344.00 ave 2344 max 2344 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 36607.0 ave 36607 max 36607 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 36607
|
||||||
|
Ave neighs/atom = 66.558182
|
||||||
|
Ave special neighs/atom = 0.36363636
|
||||||
|
Neighbor list builds = 847
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:16
|
||||||
@ -0,0 +1,218 @@
|
|||||||
|
LAMMPS (10 Mar 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# sample surface deposition script for molecules
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style bond
|
||||||
|
boundary p p f
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 5 0 5 0 10
|
||||||
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||||
|
1 by 1 by 4 MPI processor grid
|
||||||
|
|
||||||
|
region substrate block INF INF INF INF INF 3
|
||||||
|
create_atoms 1 region substrate
|
||||||
|
Created 350 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
pair_coeff 1 2 1.0 1.0 5.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 5.0 1.0
|
||||||
|
|
||||||
|
neigh_modify delay 0
|
||||||
|
|
||||||
|
molecule dimer molecule.dimer
|
||||||
|
Read molecule template dimer:
|
||||||
|
1 molecules
|
||||||
|
2 atoms with max type 3
|
||||||
|
1 bonds with max type 1
|
||||||
|
0 angles with max type 0
|
||||||
|
0 dihedrals with max type 0
|
||||||
|
0 impropers with max type 0
|
||||||
|
region slab block 0 5 0 5 8 9
|
||||||
|
|
||||||
|
group addatoms empty
|
||||||
|
0 atoms in group addatoms
|
||||||
|
region mobile block 0 5 0 5 2 INF
|
||||||
|
group mobile region mobile
|
||||||
|
150 atoms in group mobile
|
||||||
|
|
||||||
|
compute add addatoms temp
|
||||||
|
compute_modify add dynamic/dof yes extra/dof 0
|
||||||
|
|
||||||
|
fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
|
||||||
|
create bodies CPU = 0.000 seconds
|
||||||
|
0 rigid bodies with 0 atoms
|
||||||
|
1.0000000 = max distance from body owner to body atom
|
||||||
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||||
|
fix 3 mobile nve
|
||||||
|
|
||||||
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||||
|
fix 5 addatoms wall/reflect zhi EDGE
|
||||||
|
|
||||||
|
thermo_style custom step atoms temp epair etotal press
|
||||||
|
thermo 100
|
||||||
|
thermo_modify temp add lost/bond ignore lost warn
|
||||||
|
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.deposit.atom
|
||||||
|
|
||||||
|
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.3
|
||||||
|
ghost atom cutoff = 5.3
|
||||||
|
binsize = 2.65, bins = 3 3 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
||||||
|
Step Atoms Temp E_pair TotEng Press
|
||||||
|
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||||
|
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
||||||
|
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
||||||
|
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
||||||
|
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
||||||
|
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
||||||
|
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
||||||
|
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
||||||
|
800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282
|
||||||
|
900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928
|
||||||
|
1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047
|
||||||
|
1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289
|
||||||
|
1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821
|
||||||
|
1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688
|
||||||
|
1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401
|
||||||
|
1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986
|
||||||
|
1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779
|
||||||
|
1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111
|
||||||
|
1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786
|
||||||
|
1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098
|
||||||
|
2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072
|
||||||
|
2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411
|
||||||
|
2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854
|
||||||
|
2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918
|
||||||
|
2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214
|
||||||
|
2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183
|
||||||
|
2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893
|
||||||
|
2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506
|
||||||
|
2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082
|
||||||
|
2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652
|
||||||
|
3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355
|
||||||
|
3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541
|
||||||
|
3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248
|
||||||
|
3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819
|
||||||
|
3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309
|
||||||
|
3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397
|
||||||
|
3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391
|
||||||
|
3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397
|
||||||
|
3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111
|
||||||
|
3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465
|
||||||
|
4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933
|
||||||
|
4100 432 0.44820466 -6.640222 -6.5338771 -0.805972
|
||||||
|
4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414
|
||||||
|
4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484
|
||||||
|
4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062
|
||||||
|
4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194
|
||||||
|
4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114
|
||||||
|
4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577
|
||||||
|
4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746
|
||||||
|
4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416
|
||||||
|
5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399
|
||||||
|
5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755
|
||||||
|
5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092
|
||||||
|
5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134
|
||||||
|
5400 458 0.37764326 -6.661431 -6.550117 -0.72187808
|
||||||
|
5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745
|
||||||
|
5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454
|
||||||
|
5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312
|
||||||
|
5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125
|
||||||
|
5900 468 0.346812 -6.681215 -6.57191 -0.81184233
|
||||||
|
6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821
|
||||||
|
6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598
|
||||||
|
6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526
|
||||||
|
6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174
|
||||||
|
6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407
|
||||||
|
6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289
|
||||||
|
6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442
|
||||||
|
6700 484 0.37615026 -6.722917 -6.592741 -0.76534055
|
||||||
|
6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211
|
||||||
|
6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458
|
||||||
|
7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555
|
||||||
|
7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708
|
||||||
|
7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153
|
||||||
|
7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931
|
||||||
|
7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391
|
||||||
|
7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083
|
||||||
|
7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572
|
||||||
|
7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335
|
||||||
|
7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197
|
||||||
|
7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073
|
||||||
|
8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575
|
||||||
|
8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257
|
||||||
|
8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132
|
||||||
|
8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415
|
||||||
|
8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921
|
||||||
|
8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077
|
||||||
|
8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137
|
||||||
|
8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836
|
||||||
|
8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107
|
||||||
|
8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959
|
||||||
|
9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529
|
||||||
|
9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692
|
||||||
|
9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911
|
||||||
|
9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935
|
||||||
|
9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598
|
||||||
|
9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851
|
||||||
|
9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104
|
||||||
|
9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581
|
||||||
|
9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905
|
||||||
|
9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157
|
||||||
|
10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157
|
||||||
|
Loop time of 16.1559 on 4 procs for 10000 steps with 550 atoms
|
||||||
|
|
||||||
|
Performance: 267395.139 tau/day, 618.970 timesteps/s
|
||||||
|
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0035574 | 2.5467 | 7.5373 | 192.6 | 15.76
|
||||||
|
Bond | 0.0022929 | 0.0073138 | 0.019471 | 8.3 | 0.05
|
||||||
|
Neigh | 0.018645 | 1.2357 | 3.8167 | 138.4 | 7.65
|
||||||
|
Comm | 1.1946 | 6.6335 | 11.87 | 158.8 | 41.06
|
||||||
|
Output | 0.010714 | 0.014391 | 0.020006 | 3.2 | 0.09
|
||||||
|
Modify | 3.4474 | 5.6081 | 11.47 | 143.2 | 34.71
|
||||||
|
Other | | 0.1102 | | | 0.68
|
||||||
|
|
||||||
|
Nlocal: 137.500 ave 299 max 2 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 1903.75 ave 2686 max 529 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||||
|
Neighs: 9209.75 ave 23206 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 36839
|
||||||
|
Ave neighs/atom = 66.980000
|
||||||
|
Ave special neighs/atom = 0.36363636
|
||||||
|
Neighbor list builds = 829
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:16
|
||||||
@ -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] \
|
||||||
|
|||||||
@ -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.
|
||||||
|
|
||||||
|
|||||||
@ -1061,7 +1061,7 @@ bool lmp_gpu_config(const std::string &category, const std::string &setting)
|
|||||||
return setting == "opencl";
|
return setting == "opencl";
|
||||||
#elif defined(USE_HIP)
|
#elif defined(USE_HIP)
|
||||||
return setting == "hip";
|
return setting == "hip";
|
||||||
#elif defined(USE_CUDA)
|
#elif defined(USE_CUDA) || defined(USE_CUDART)
|
||||||
return setting == "cuda";
|
return setting == "cuda";
|
||||||
#endif
|
#endif
|
||||||
return false;
|
return false;
|
||||||
|
|||||||
@ -26,10 +26,10 @@ _texture_2d( pos_tex,int4);
|
|||||||
|
|
||||||
// LJ quantities scaled by epsilon and rmin = sigma*2^1/6 (see src/pair_lj_cubic.h)
|
// LJ quantities scaled by epsilon and rmin = sigma*2^1/6 (see src/pair_lj_cubic.h)
|
||||||
|
|
||||||
#define _RT6TWO (numtyp)1.1224621
|
#define _RT6TWO (numtyp)1.1224620483093730 /* 2^1/6 */
|
||||||
#define _PHIS (numtyp)-0.7869823 /* energy at s */
|
#define _PHIS (numtyp)-0.7869822485207097 /* energy at s */
|
||||||
#define _DPHIDS (numtyp)2.6899009 /* gradient at s */
|
#define _DPHIDS (numtyp)2.6899008972047196 /* gradient at s */
|
||||||
#define _A3 (numtyp)27.93357 /* cubic coefficient */
|
#define _A3 (numtyp)27.9335700460986445 /* cubic coefficient */
|
||||||
|
|
||||||
__kernel void k_lj_cubic(const __global numtyp4 *restrict x_,
|
__kernel void k_lj_cubic(const __global numtyp4 *restrict x_,
|
||||||
const __global numtyp4 *restrict lj1,
|
const __global numtyp4 *restrict lj1,
|
||||||
|
|||||||
@ -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
|
||||||
|
|||||||
@ -1747,17 +1747,23 @@ class lammps(object):
|
|||||||
|
|
||||||
# -------------------------------------------------------------------------
|
# -------------------------------------------------------------------------
|
||||||
|
|
||||||
def find_pair_neighlist(self, style, exact=True, nsub=0, request=0):
|
def find_pair_neighlist(self, style, exact=True, nsub=0, reqid=0):
|
||||||
"""Find neighbor list index of pair style neighbor list
|
"""Find neighbor list index of pair style neighbor list
|
||||||
|
|
||||||
Try finding pair instance that matches style. If exact is set, the pair must
|
Search for a neighbor list requested by a pair style instance that
|
||||||
match style exactly. If exact is 0, style must only be contained. If pair is
|
matches "style". If exact is True, the pair style name must match
|
||||||
of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
|
exactly. If exact is False, the pair style name is matched against
|
||||||
|
"style" as regular expression or sub-string. If the pair style is a
|
||||||
|
hybrid pair style, the style is instead matched against the hybrid
|
||||||
|
sub-styles. If the same pair style is used as sub-style multiple
|
||||||
|
types, you must set nsub to a value n > 0 which indicates the nth
|
||||||
|
instance of that sub-style to be used (same as for the pair_coeff
|
||||||
|
command). The default value of 0 will fail to match in that case.
|
||||||
|
|
||||||
Once the pair instance has been identified, multiple neighbor list requests
|
Once the pair style instance has been identified, it may have
|
||||||
may be found. Every neighbor list is uniquely identified by its request
|
requested multiple neighbor lists. Those are uniquely identified by
|
||||||
index. Thus, providing this request index ensures that the correct neighbor
|
a request ID > 0 as set by the pair style. Otherwise the request
|
||||||
list index is returned.
|
ID is 0.
|
||||||
|
|
||||||
:param style: name of pair style that should be searched for
|
:param style: name of pair style that should be searched for
|
||||||
:type style: string
|
:type style: string
|
||||||
@ -1765,44 +1771,58 @@ class lammps(object):
|
|||||||
:type exact: bool, optional
|
:type exact: bool, optional
|
||||||
:param nsub: match nsub-th hybrid sub-style, defaults to 0
|
:param nsub: match nsub-th hybrid sub-style, defaults to 0
|
||||||
:type nsub: int, optional
|
:type nsub: int, optional
|
||||||
:param request: index of neighbor list request, in case there are more than one, defaults to 0
|
:param reqid: list request id, > 0 in case there are more than one, defaults to 0
|
||||||
:type request: int, optional
|
:type reqid: int, optional
|
||||||
:return: neighbor list index if found, otherwise -1
|
:return: neighbor list index if found, otherwise -1
|
||||||
:rtype: int
|
:rtype: int
|
||||||
|
|
||||||
"""
|
"""
|
||||||
style = style.encode()
|
style = style.encode()
|
||||||
exact = int(exact)
|
exact = int(exact)
|
||||||
idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request)
|
idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, reqid)
|
||||||
return idx
|
return idx
|
||||||
|
|
||||||
# -------------------------------------------------------------------------
|
# -------------------------------------------------------------------------
|
||||||
|
|
||||||
def find_fix_neighlist(self, fixid, request=0):
|
def find_fix_neighlist(self, fixid, reqid=0):
|
||||||
"""Find neighbor list index of fix neighbor list
|
"""Find neighbor list index of fix neighbor list
|
||||||
|
|
||||||
|
The fix instance requesting the neighbor list is uniquely identified
|
||||||
|
by the fix ID. In case the fix has requested multiple neighbor
|
||||||
|
lists, those are uniquely identified by a request ID > 0 as set by
|
||||||
|
the fix. Otherwise the request ID is 0 (the default).
|
||||||
|
|
||||||
:param fixid: name of fix
|
:param fixid: name of fix
|
||||||
:type fixid: string
|
:type fixid: string
|
||||||
:param request: index of neighbor list request, in case there are more than one, defaults to 0
|
:param reqid: id of neighbor list request, in case there are more than one request, defaults to 0
|
||||||
:type request: int, optional
|
:type reqid: int, optional
|
||||||
:return: neighbor list index if found, otherwise -1
|
:return: neighbor list index if found, otherwise -1
|
||||||
:rtype: int
|
:rtype: int
|
||||||
|
|
||||||
"""
|
"""
|
||||||
fixid = fixid.encode()
|
fixid = fixid.encode()
|
||||||
idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request)
|
idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, reqid)
|
||||||
return idx
|
return idx
|
||||||
|
|
||||||
# -------------------------------------------------------------------------
|
# -------------------------------------------------------------------------
|
||||||
|
|
||||||
def find_compute_neighlist(self, computeid, request=0):
|
def find_compute_neighlist(self, computeid, reqid=0):
|
||||||
"""Find neighbor list index of compute neighbor list
|
"""Find neighbor list index of compute neighbor list
|
||||||
|
|
||||||
|
The compute instance requesting the neighbor list is uniquely
|
||||||
|
identified by the compute ID. In case the compute has requested
|
||||||
|
multiple neighbor lists, those are uniquely identified by a request
|
||||||
|
ID > 0 as set by the compute. Otherwise the request ID is 0 (the
|
||||||
|
default).
|
||||||
|
|
||||||
:param computeid: name of compute
|
:param computeid: name of compute
|
||||||
:type computeid: string
|
:type computeid: string
|
||||||
:param request: index of neighbor list request, in case there are more than one, defaults to 0
|
:param reqid: index of neighbor list request, in case there are more than one request, defaults to 0
|
||||||
:type request: int, optional
|
:type reqid: int, optional
|
||||||
:return: neighbor list index if found, otherwise -1
|
:return: neighbor list index if found, otherwise -1
|
||||||
:rtype: int
|
:rtype: int
|
||||||
|
|
||||||
"""
|
"""
|
||||||
computeid = computeid.encode()
|
computeid = computeid.encode()
|
||||||
idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request)
|
idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, reqid)
|
||||||
return idx
|
return idx
|
||||||
|
|||||||
@ -52,7 +52,9 @@ class NeighList:
|
|||||||
|
|
||||||
def get(self, element):
|
def get(self, element):
|
||||||
"""
|
"""
|
||||||
:return: tuple with atom local index, numpy array of neighbor local atom indices
|
Access a specific neighbor list entry. "element" must be a number from 0 to the size-1 of the list
|
||||||
|
|
||||||
|
:return: tuple with atom local index, number of neighbors and ctypes pointer to neighbor's local atom indices
|
||||||
:rtype: (int, int, ctypes.POINTER(c_int))
|
:rtype: (int, int, ctypes.POINTER(c_int))
|
||||||
"""
|
"""
|
||||||
iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
|
iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
|
||||||
@ -71,3 +73,20 @@ class NeighList:
|
|||||||
|
|
||||||
for ii in range(inum):
|
for ii in range(inum):
|
||||||
yield self.get(ii)
|
yield self.get(ii)
|
||||||
|
|
||||||
|
def find(self, iatom):
|
||||||
|
"""
|
||||||
|
Find the neighbor list for a specific (local) atom iatom.
|
||||||
|
If there is no list for iatom, (-1, None) is returned.
|
||||||
|
|
||||||
|
:return: tuple with number of neighbors and ctypes pointer to neighbor's local atom indices
|
||||||
|
:rtype: (int, ctypes.POINTER(c_int))
|
||||||
|
"""
|
||||||
|
|
||||||
|
inum = self.size
|
||||||
|
for ii in range(inum):
|
||||||
|
idx, numneigh, neighbors = self.get(ii)
|
||||||
|
if idx == iatom:
|
||||||
|
return numneigh, neighbors
|
||||||
|
|
||||||
|
return -1, None
|
||||||
|
|||||||
@ -331,8 +331,25 @@ class NumPyNeighList(NeighList):
|
|||||||
|
|
||||||
def get(self, element):
|
def get(self, element):
|
||||||
"""
|
"""
|
||||||
|
Access a specific neighbor list entry. "element" must be a number from 0 to the size-1 of the list
|
||||||
|
|
||||||
:return: tuple with atom local index, numpy array of neighbor local atom indices
|
:return: tuple with atom local index, numpy array of neighbor local atom indices
|
||||||
:rtype: (int, numpy.array)
|
:rtype: (int, numpy.array)
|
||||||
"""
|
"""
|
||||||
iatom, neighbors = self.lmp.numpy.get_neighlist_element_neighbors(self.idx, element)
|
iatom, neighbors = self.lmp.numpy.get_neighlist_element_neighbors(self.idx, element)
|
||||||
return iatom, neighbors
|
return iatom, neighbors
|
||||||
|
|
||||||
|
def find(self, iatom):
|
||||||
|
"""
|
||||||
|
Find the neighbor list for a specific (local) atom iatom.
|
||||||
|
If there is no list for iatom, None is returned.
|
||||||
|
|
||||||
|
:return: numpy array of neighbor local atom indices
|
||||||
|
:rtype: numpy.array or None
|
||||||
|
"""
|
||||||
|
inum = self.size
|
||||||
|
for ii in range(inum):
|
||||||
|
idx, neighbors = self.get(ii)
|
||||||
|
if idx == iatom:
|
||||||
|
return neighbors
|
||||||
|
return None
|
||||||
|
|||||||
@ -11,20 +11,20 @@
|
|||||||
|
|
||||||
#include "pair_lj_class2.h"
|
#include "pair_lj_class2.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 "neighbor.h"
|
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "neigh_request.h"
|
|
||||||
#include "update.h"
|
|
||||||
#include "respa.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;
|
||||||
@ -36,6 +36,7 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
|
|||||||
respa_enable = 1;
|
respa_enable = 1;
|
||||||
writedata = 1;
|
writedata = 1;
|
||||||
centroidstressflag = CENTROID_SAME;
|
centroidstressflag = CENTROID_SAME;
|
||||||
|
cut_respa = nullptr;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -16,25 +16,24 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "pair_lj_class2_gpu.h"
|
#include "pair_lj_class2_gpu.h"
|
||||||
#include <cmath>
|
|
||||||
#include <cstdio>
|
|
||||||
|
|
||||||
#include <cstring>
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
#include "force.h"
|
#include "force.h"
|
||||||
#include "neighbor.h"
|
#include "gpu_extra.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "integrate.h"
|
#include "integrate.h"
|
||||||
#include "memory.h"
|
#include "memory.h"
|
||||||
#include "error.h"
|
#include "neigh_list.h"
|
||||||
#include "neigh_request.h"
|
#include "neigh_request.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "suffix.h"
|
||||||
#include "universe.h"
|
#include "universe.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
#include "domain.h"
|
|
||||||
#include "gpu_extra.h"
|
#include <cmath>
|
||||||
#include "suffix.h"
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -64,6 +63,7 @@ double lj96_gpu_bytes();
|
|||||||
|
|
||||||
PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_FORCE)
|
PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_FORCE)
|
||||||
{
|
{
|
||||||
|
respa_enable = 0;
|
||||||
reinitflag = 0;
|
reinitflag = 0;
|
||||||
cpu_time = 0.0;
|
cpu_time = 0.0;
|
||||||
suffix_flag |= Suffix::GPU;
|
suffix_flag |= Suffix::GPU;
|
||||||
|
|||||||
@ -17,25 +17,24 @@
|
|||||||
|
|
||||||
#include "pair_lj_cubic_gpu.h"
|
#include "pair_lj_cubic_gpu.h"
|
||||||
|
|
||||||
#include <cmath>
|
|
||||||
#include <cstdio>
|
|
||||||
#include <cstring>
|
|
||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
#include "force.h"
|
#include "force.h"
|
||||||
#include "neighbor.h"
|
#include "gpu_extra.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "integrate.h"
|
#include "integrate.h"
|
||||||
#include "memory.h"
|
#include "memory.h"
|
||||||
#include "error.h"
|
#include "neigh_list.h"
|
||||||
#include "neigh_request.h"
|
#include "neigh_request.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "suffix.h"
|
||||||
#include "universe.h"
|
#include "universe.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
#include "domain.h"
|
|
||||||
#include "gpu_extra.h"
|
#include <cmath>
|
||||||
#include "suffix.h"
|
#include <cstring>
|
||||||
|
|
||||||
#include "pair_lj_cubic_const.h"
|
#include "pair_lj_cubic_const.h"
|
||||||
|
|
||||||
|
|||||||
@ -54,7 +54,8 @@ enum {XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};
|
|||||||
enum {NONE,CONSTANT,EQUAL};
|
enum {NONE,CONSTANT,EQUAL};
|
||||||
enum {DAMPING_NONE, VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI};
|
enum {DAMPING_NONE, VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI};
|
||||||
enum {TANGENTIAL_NONE, TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY,
|
enum {TANGENTIAL_NONE, TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY,
|
||||||
TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE};
|
TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE,
|
||||||
|
TANGENTIAL_MINDLIN_FORCE, TANGENTIAL_MINDLIN_RESCALE_FORCE};
|
||||||
enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL};
|
enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL};
|
||||||
enum {ROLL_NONE, ROLL_SDS};
|
enum {ROLL_NONE, ROLL_SDS};
|
||||||
|
|
||||||
@ -70,6 +71,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
error->all(FLERR,"Fix wall/gran requires atom style sphere");
|
error->all(FLERR,"Fix wall/gran requires atom style sphere");
|
||||||
|
|
||||||
create_attribute = 1;
|
create_attribute = 1;
|
||||||
|
limit_damping = 0;
|
||||||
|
|
||||||
// set interaction style
|
// set interaction style
|
||||||
// disable bonded/history option for now
|
// disable bonded/history option for now
|
||||||
@ -90,7 +92,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// wall/particle coefficients
|
// wall/particle coefficients
|
||||||
|
|
||||||
int iarg;
|
int iarg;
|
||||||
|
|
||||||
if (pairstyle != GRANULAR) {
|
if (pairstyle != GRANULAR) {
|
||||||
size_history = 3;
|
size_history = 3;
|
||||||
if (narg < 11) error->all(FLERR,"Illegal fix wall/gran command");
|
if (narg < 11) error->all(FLERR,"Illegal fix wall/gran command");
|
||||||
@ -118,6 +119,12 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
kt /= force->nktv2p;
|
kt /= force->nktv2p;
|
||||||
}
|
}
|
||||||
iarg = 10;
|
iarg = 10;
|
||||||
|
|
||||||
|
if (strcmp(arg[iarg],"limit_damping") == 0) {
|
||||||
|
limit_damping = 1;
|
||||||
|
iarg += 1;
|
||||||
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
iarg = 4;
|
iarg = 4;
|
||||||
damping_model = VISCOELASTIC;
|
damping_model = VISCOELASTIC;
|
||||||
@ -211,7 +218,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
iarg += 4;
|
iarg += 4;
|
||||||
} else if ((strcmp(arg[iarg+1], "linear_history") == 0) ||
|
} else if ((strcmp(arg[iarg+1], "linear_history") == 0) ||
|
||||||
(strcmp(arg[iarg+1], "mindlin") == 0) ||
|
(strcmp(arg[iarg+1], "mindlin") == 0) ||
|
||||||
(strcmp(arg[iarg+1], "mindlin_rescale") == 0)) {
|
(strcmp(arg[iarg+1], "mindlin_rescale") == 0) ||
|
||||||
|
(strcmp(arg[iarg+1], "mindlin/force") == 0) ||
|
||||||
|
(strcmp(arg[iarg+1], "mindlin_rescale/force") == 0)) {
|
||||||
if (iarg + 4 >= narg)
|
if (iarg + 4 >= narg)
|
||||||
error->all(FLERR,"Illegal pair_coeff command, "
|
error->all(FLERR,"Illegal pair_coeff command, "
|
||||||
"not enough parameters provided for tangential model");
|
"not enough parameters provided for tangential model");
|
||||||
@ -221,8 +230,14 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
tangential_model = TANGENTIAL_MINDLIN;
|
tangential_model = TANGENTIAL_MINDLIN;
|
||||||
else if (strcmp(arg[iarg+1], "mindlin_rescale") == 0)
|
else if (strcmp(arg[iarg+1], "mindlin_rescale") == 0)
|
||||||
tangential_model = TANGENTIAL_MINDLIN_RESCALE;
|
tangential_model = TANGENTIAL_MINDLIN_RESCALE;
|
||||||
|
else if (strcmp(arg[iarg+1], "mindlin/force") == 0)
|
||||||
|
tangential_model = TANGENTIAL_MINDLIN_FORCE;
|
||||||
|
else if (strcmp(arg[iarg+1], "mindlin_rescale/force") == 0)
|
||||||
|
tangential_model = TANGENTIAL_MINDLIN_RESCALE_FORCE;
|
||||||
if ((tangential_model == TANGENTIAL_MINDLIN ||
|
if ((tangential_model == TANGENTIAL_MINDLIN ||
|
||||||
tangential_model == TANGENTIAL_MINDLIN_RESCALE) &&
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_FORCE ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) &&
|
||||||
(strcmp(arg[iarg+2], "NULL") == 0)) {
|
(strcmp(arg[iarg+2], "NULL") == 0)) {
|
||||||
if (normal_model == NORMAL_HERTZ || normal_model == NORMAL_HOOKE) {
|
if (normal_model == NORMAL_HERTZ || normal_model == NORMAL_HOOKE) {
|
||||||
error->all(FLERR, "NULL setting for Mindlin tangential "
|
error->all(FLERR, "NULL setting for Mindlin tangential "
|
||||||
@ -293,13 +308,27 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
strcmp(arg[iarg], "zcylinder") == 0 ||
|
strcmp(arg[iarg], "zcylinder") == 0 ||
|
||||||
strcmp(arg[iarg], "region") == 0) {
|
strcmp(arg[iarg], "region") == 0) {
|
||||||
break;
|
break;
|
||||||
|
} else if (strcmp(arg[iarg],"limit_damping") == 0) {
|
||||||
|
limit_damping = 1;
|
||||||
|
iarg += 1;
|
||||||
} else {
|
} else {
|
||||||
error->all(FLERR, "Illegal fix wall/gran command");
|
error->all(FLERR, "Illegal fix wall/gran command");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
size_history = 3*tangential_history + 3*roll_history + twist_history;
|
size_history = 3*tangential_history + 3*roll_history + twist_history;
|
||||||
|
//Unlike the pair style, the wall style does not have a 'touch'
|
||||||
|
//array. Hence, an additional entry in the history is used to
|
||||||
|
//determine if particles previously contacted for JKR cohesion purposes.
|
||||||
if (normal_model == JKR) size_history += 1;
|
if (normal_model == JKR) size_history += 1;
|
||||||
if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) size_history += 1;
|
if (tangential_model == TANGENTIAL_MINDLIN_RESCALE ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) size_history += 1;
|
||||||
|
|
||||||
|
if (limit_damping && normal_model == JKR)
|
||||||
|
error->all(FLERR,"Illegal pair_coeff command, "
|
||||||
|
"cannot limit damping with JRK model");
|
||||||
|
if (limit_damping && normal_model == DMT)
|
||||||
|
error->all(FLERR,"Illegal pair_coeff command, "
|
||||||
|
"Cannot limit damping with DMT model");
|
||||||
}
|
}
|
||||||
|
|
||||||
// wallstyle args
|
// wallstyle args
|
||||||
@ -475,6 +504,7 @@ void FixWallGran::init()
|
|||||||
if (modify->fix[i]->rigid_flag) break;
|
if (modify->fix[i]->rigid_flag) break;
|
||||||
if (i < modify->nfix) fix_rigid = modify->fix[i];
|
if (i < modify->nfix) fix_rigid = modify->fix[i];
|
||||||
|
|
||||||
|
if(pairstyle == GRANULAR) {
|
||||||
tangential_history_index = 0;
|
tangential_history_index = 0;
|
||||||
if (roll_history) {
|
if (roll_history) {
|
||||||
if (tangential_history) roll_history_index = 3;
|
if (tangential_history) roll_history_index = 3;
|
||||||
@ -495,7 +525,8 @@ void FixWallGran::init()
|
|||||||
roll_history_index += 1;
|
roll_history_index += 1;
|
||||||
twist_history_index += 1;
|
twist_history_index += 1;
|
||||||
}
|
}
|
||||||
if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) {
|
if (tangential_model == TANGENTIAL_MINDLIN_RESCALE ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE) {
|
||||||
roll_history_index += 1;
|
roll_history_index += 1;
|
||||||
twist_history_index += 1;
|
twist_history_index += 1;
|
||||||
}
|
}
|
||||||
@ -507,6 +538,7 @@ void FixWallGran::init()
|
|||||||
4.8218*pow(cor,6);
|
4.8218*pow(cor,6);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -762,6 +794,7 @@ void FixWallGran::hooke(double rsq, double dx, double dy, double dz,
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radius-r)*rinv - damp;
|
ccel = kn*(radius-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -854,6 +887,7 @@ void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radius-r)*rinv - damp;
|
ccel = kn*(radius-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -985,6 +1019,7 @@ void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
|
|||||||
if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius);
|
if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius);
|
||||||
else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius));
|
else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius));
|
||||||
ccel *= polyhertz;
|
ccel *= polyhertz;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -1103,7 +1138,8 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
double signtwist, magtwist, magtortwist, Mtcrit;
|
double signtwist, magtwist, magtortwist, Mtcrit;
|
||||||
double tortwist1, tortwist2, tortwist3;
|
double tortwist1, tortwist2, tortwist3;
|
||||||
|
|
||||||
double shrmag,rsht;
|
double shrmag,rsht,prjmag;
|
||||||
|
bool frameupdate;
|
||||||
|
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
E = normal_coeffs[0];
|
E = normal_coeffs[0];
|
||||||
@ -1178,11 +1214,18 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
Fdamp = -damp_normal_prefactor*vnnr;
|
Fdamp = -damp_normal_prefactor*vnnr;
|
||||||
|
|
||||||
Fntot = Fne + Fdamp;
|
Fntot = Fne + Fdamp;
|
||||||
|
if (limit_damping && (Fntot < 0.0)) Fntot = 0.0;
|
||||||
|
|
||||||
//****************************************
|
//****************************************
|
||||||
// tangential force, including history effects
|
// tangential force, including history effects
|
||||||
//****************************************
|
//****************************************
|
||||||
|
|
||||||
|
// For linear, mindlin, mindlin_rescale:
|
||||||
|
// history = cumulative tangential displacement
|
||||||
|
//
|
||||||
|
// For mindlin/force, mindlin_rescale/force:
|
||||||
|
// history = cumulative tangential elastic force
|
||||||
|
|
||||||
// tangential component
|
// tangential component
|
||||||
vt1 = vr1 - vn1;
|
vt1 = vr1 - vn1;
|
||||||
vt2 = vr2 - vn2;
|
vt2 = vr2 - vn2;
|
||||||
@ -1224,69 +1267,115 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
int thist2 = thist1 + 1;
|
int thist2 = thist1 + 1;
|
||||||
|
|
||||||
if (tangential_history) {
|
if (tangential_history) {
|
||||||
if (tangential_model == TANGENTIAL_MINDLIN) {
|
if (tangential_model == TANGENTIAL_MINDLIN ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_FORCE) {
|
||||||
k_tangential *= a;
|
k_tangential *= a;
|
||||||
}
|
}
|
||||||
else if (tangential_model == TANGENTIAL_MINDLIN_RESCALE) {
|
else if (tangential_model ==
|
||||||
|
TANGENTIAL_MINDLIN_RESCALE ||
|
||||||
|
tangential_model ==
|
||||||
|
TANGENTIAL_MINDLIN_RESCALE_FORCE){
|
||||||
k_tangential *= a;
|
k_tangential *= a;
|
||||||
if (a < history[3]) { //On unloading, rescale the shear displacements
|
// on unloading, rescale the shear displacements/force
|
||||||
|
if (a < history[thist2+1]) {
|
||||||
double factor = a/history[thist2+1];
|
double factor = a/history[thist2+1];
|
||||||
history[thist0] *= factor;
|
history[thist0] *= factor;
|
||||||
history[thist1] *= factor;
|
history[thist1] *= factor;
|
||||||
history[thist2] *= factor;
|
history[thist2] *= factor;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
shrmag = sqrt(history[thist0]*history[thist0] +
|
|
||||||
history[thist1]*history[thist1] +
|
|
||||||
history[thist2]*history[thist2]);
|
|
||||||
|
|
||||||
// rotate and update displacements.
|
// rotate and update displacements.
|
||||||
// see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235
|
// see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235
|
||||||
if (history_update) {
|
if (history_update) {
|
||||||
rsht = history[thist0]*nx + history[thist1]*ny + history[thist2]*nz;
|
rsht = history[thist0]*nx + history[thist1]*ny + history[thist2]*nz;
|
||||||
if (fabs(rsht) < EPSILON) rsht = 0;
|
if (tangential_model == TANGENTIAL_MINDLIN_FORCE ||
|
||||||
if (rsht > 0) {
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE)
|
||||||
// if rhst == shrmag, contacting pair has rotated 90 deg in one step,
|
frameupdate = fabs(rsht) > EPSILON*Fscrit;
|
||||||
// in which case you deserve a crash!
|
else
|
||||||
scalefac = shrmag/(shrmag - rsht);
|
frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit;
|
||||||
|
if (frameupdate) {
|
||||||
|
shrmag = sqrt(history[thist0]*history[thist0] +
|
||||||
|
history[thist1]*history[thist1] +
|
||||||
|
history[thist2]*history[thist2]);
|
||||||
|
// projection
|
||||||
history[thist0] -= rsht*nx;
|
history[thist0] -= rsht*nx;
|
||||||
history[thist1] -= rsht*ny;
|
history[thist1] -= rsht*ny;
|
||||||
history[thist2] -= rsht*nz;
|
history[thist2] -= rsht*nz;
|
||||||
|
|
||||||
// also rescale to preserve magnitude
|
// also rescale to preserve magnitude
|
||||||
|
prjmag = sqrt(history[thist0]*history[thist0] +
|
||||||
|
history[thist1]*history[thist1] + history[thist2]*history[thist2]);
|
||||||
|
if (prjmag > 0) scalefac = shrmag/prjmag;
|
||||||
|
else scalefac = 0;
|
||||||
history[thist0] *= scalefac;
|
history[thist0] *= scalefac;
|
||||||
history[thist1] *= scalefac;
|
history[thist1] *= scalefac;
|
||||||
history[thist2] *= scalefac;
|
history[thist2] *= scalefac;
|
||||||
}
|
}
|
||||||
// update history
|
// update history
|
||||||
|
if (tangential_model == TANGENTIAL_HISTORY ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE) {
|
||||||
history[thist0] += vtr1*dt;
|
history[thist0] += vtr1*dt;
|
||||||
history[thist1] += vtr2*dt;
|
history[thist1] += vtr2*dt;
|
||||||
history[thist2] += vtr3*dt;
|
history[thist2] += vtr3*dt;
|
||||||
|
} else{
|
||||||
|
// tangential force
|
||||||
|
// see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46
|
||||||
|
history[thist0] -= k_tangential*vtr1*dt;
|
||||||
|
history[thist1] -= k_tangential*vtr2*dt;
|
||||||
|
history[thist2] -= k_tangential*vtr3*dt;
|
||||||
|
}
|
||||||
|
if (tangential_model == TANGENTIAL_MINDLIN_RESCALE ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE_FORCE)
|
||||||
|
history[thist2+1] = a;
|
||||||
}
|
}
|
||||||
|
|
||||||
// tangential forces = history + tangential velocity damping
|
// tangential forces = history + tangential velocity damping
|
||||||
|
if (tangential_model == TANGENTIAL_HISTORY ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN_RESCALE) {
|
||||||
fs1 = -k_tangential*history[thist0] - damp_tangential*vtr1;
|
fs1 = -k_tangential*history[thist0] - damp_tangential*vtr1;
|
||||||
fs2 = -k_tangential*history[thist1] - damp_tangential*vtr2;
|
fs2 = -k_tangential*history[thist1] - damp_tangential*vtr2;
|
||||||
fs3 = -k_tangential*history[thist2] - damp_tangential*vtr3;
|
fs3 = -k_tangential*history[thist2] - damp_tangential*vtr3;
|
||||||
|
} else {
|
||||||
|
fs1 = history[thist0] - damp_tangential*vtr1;
|
||||||
|
fs2 = history[thist1] - damp_tangential*vtr2;
|
||||||
|
fs3 = history[thist2] - damp_tangential*vtr3;
|
||||||
|
}
|
||||||
|
|
||||||
// rescale frictional displacements and forces if needed
|
// rescale frictional displacements and forces if needed
|
||||||
Fscrit = tangential_coeffs[2] * Fncrit;
|
Fscrit = tangential_coeffs[2] * Fncrit;
|
||||||
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
|
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
|
||||||
if (fs > Fscrit) {
|
if (fs > Fscrit) {
|
||||||
|
shrmag = sqrt(history[thist0]*history[thist0] +
|
||||||
|
history[thist1]*history[thist1] +
|
||||||
|
history[thist2]*history[thist2]);
|
||||||
if (shrmag != 0.0) {
|
if (shrmag != 0.0) {
|
||||||
|
if (tangential_model == TANGENTIAL_HISTORY ||
|
||||||
|
tangential_model == TANGENTIAL_MINDLIN ||
|
||||||
|
tangential_model ==
|
||||||
|
TANGENTIAL_MINDLIN_RESCALE) {
|
||||||
history[thist0] = -1.0/k_tangential*(Fscrit*fs1/fs +
|
history[thist0] = -1.0/k_tangential*(Fscrit*fs1/fs +
|
||||||
damp_tangential*vtr1);
|
damp_tangential*vtr1);
|
||||||
history[thist1] = -1.0/k_tangential*(Fscrit*fs2/fs +
|
history[thist1] = -1.0/k_tangential*(Fscrit*fs2/fs +
|
||||||
damp_tangential*vtr2);
|
damp_tangential*vtr2);
|
||||||
history[thist2] = -1.0/k_tangential*(Fscrit*fs3/fs +
|
history[thist2] = -1.0/k_tangential*(Fscrit*fs3/fs +
|
||||||
damp_tangential*vtr3);
|
damp_tangential*vtr3);
|
||||||
|
} else {
|
||||||
|
history[thist0] = Fscrit*fs1/fs + damp_tangential*vtr1;
|
||||||
|
history[thist1] = Fscrit*fs2/fs + damp_tangential*vtr2;
|
||||||
|
history[thist2] = Fscrit*fs3/fs + damp_tangential*vtr3;
|
||||||
|
}
|
||||||
fs1 *= Fscrit/fs;
|
fs1 *= Fscrit/fs;
|
||||||
fs2 *= Fscrit/fs;
|
fs2 *= Fscrit/fs;
|
||||||
fs3 *= Fscrit/fs;
|
fs3 *= Fscrit/fs;
|
||||||
} else fs1 = fs2 = fs3 = 0.0;
|
} else fs1 = fs2 = fs3 = 0.0;
|
||||||
}
|
}
|
||||||
} else { // classic pair gran/hooke (no history)
|
} else { // classic pair gran/hooke (no history)
|
||||||
fs = meff*damp_tangential*vrel;
|
fs = damp_tangential*vrel;
|
||||||
if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel;
|
if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel;
|
||||||
else Ft = 0.0;
|
else Ft = 0.0;
|
||||||
fs1 = -Ft*vtr1;
|
fs1 = -Ft*vtr1;
|
||||||
fs2 = -Ft*vtr2;
|
fs2 = -Ft*vtr2;
|
||||||
@ -1297,14 +1386,14 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
// rolling resistance
|
// rolling resistance
|
||||||
//****************************************
|
//****************************************
|
||||||
|
|
||||||
if (roll_model != ROLL_NONE || twist_model != NONE) {
|
if (roll_model != ROLL_NONE || twist_model != TWIST_NONE) {
|
||||||
relrot1 = omega[0];
|
relrot1 = omega[0];
|
||||||
relrot2 = omega[1];
|
relrot2 = omega[1];
|
||||||
relrot3 = omega[2];
|
relrot3 = omega[2];
|
||||||
}
|
}
|
||||||
if (roll_model != ROLL_NONE) {
|
if (roll_model != ROLL_NONE) {
|
||||||
|
// rolling velocity,
|
||||||
// rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
|
// see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
|
||||||
// This is different from the Marshall papers,
|
// This is different from the Marshall papers,
|
||||||
// which use the Bagi/Kuhn formulation
|
// which use the Bagi/Kuhn formulation
|
||||||
// for rolling velocity (see Wang et al for why the latter is wrong)
|
// for rolling velocity (see Wang et al for why the latter is wrong)
|
||||||
@ -1316,21 +1405,29 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
int rhist1 = rhist0 + 1;
|
int rhist1 = rhist0 + 1;
|
||||||
int rhist2 = rhist1 + 1;
|
int rhist2 = rhist1 + 1;
|
||||||
|
|
||||||
// rolling displacement
|
k_roll = roll_coeffs[0];
|
||||||
|
damp_roll = roll_coeffs[1];
|
||||||
|
Frcrit = roll_coeffs[2] * Fncrit;
|
||||||
|
|
||||||
|
if (history_update) {
|
||||||
|
rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz;
|
||||||
|
frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit;
|
||||||
|
if (frameupdate) { // rotate into tangential plane
|
||||||
rollmag = sqrt(history[rhist0]*history[rhist0] +
|
rollmag = sqrt(history[rhist0]*history[rhist0] +
|
||||||
history[rhist1]*history[rhist1] +
|
history[rhist1]*history[rhist1] +
|
||||||
history[rhist2]*history[rhist2]);
|
history[rhist2]*history[rhist2]);
|
||||||
|
// projection
|
||||||
rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz;
|
|
||||||
|
|
||||||
if (history_update) {
|
|
||||||
if (fabs(rolldotn) < EPSILON) rolldotn = 0;
|
|
||||||
if (rolldotn > 0) { // rotate into tangential plane
|
|
||||||
scalefac = rollmag/(rollmag - rolldotn);
|
|
||||||
history[rhist0] -= rolldotn*nx;
|
history[rhist0] -= rolldotn*nx;
|
||||||
history[rhist1] -= rolldotn*ny;
|
history[rhist1] -= rolldotn*ny;
|
||||||
history[rhist2] -= rolldotn*nz;
|
history[rhist2] -= rolldotn*nz;
|
||||||
|
|
||||||
// also rescale to preserve magnitude
|
// also rescale to preserve magnitude
|
||||||
|
prjmag = sqrt(history[rhist0]*history[rhist0] +
|
||||||
|
history[rhist1]*history[rhist1] +
|
||||||
|
history[rhist2]*history[rhist2]);
|
||||||
|
|
||||||
|
if (prjmag > 0) scalefac = rollmag/prjmag;
|
||||||
|
else scalefac = 0;
|
||||||
history[rhist0] *= scalefac;
|
history[rhist0] *= scalefac;
|
||||||
history[rhist1] *= scalefac;
|
history[rhist1] *= scalefac;
|
||||||
history[rhist2] *= scalefac;
|
history[rhist2] *= scalefac;
|
||||||
@ -1340,17 +1437,16 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||||||
history[rhist2] += vrl3*dt;
|
history[rhist2] += vrl3*dt;
|
||||||
}
|
}
|
||||||
|
|
||||||
k_roll = roll_coeffs[0];
|
|
||||||
damp_roll = roll_coeffs[1];
|
|
||||||
fr1 = -k_roll*history[rhist0] - damp_roll*vrl1;
|
fr1 = -k_roll*history[rhist0] - damp_roll*vrl1;
|
||||||
fr2 = -k_roll*history[rhist1] - damp_roll*vrl2;
|
fr2 = -k_roll*history[rhist1] - damp_roll*vrl2;
|
||||||
fr3 = -k_roll*history[rhist2] - damp_roll*vrl3;
|
fr3 = -k_roll*history[rhist2] - damp_roll*vrl3;
|
||||||
|
|
||||||
// rescale frictional displacements and forces if needed
|
// rescale frictional displacements and forces if needed
|
||||||
Frcrit = roll_coeffs[2] * Fncrit;
|
|
||||||
|
|
||||||
fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3);
|
fr = sqrt(fr1*fr1 + fr2*fr2 + fr3*fr3);
|
||||||
if (fr > Frcrit) {
|
if (fr > Frcrit) {
|
||||||
|
rollmag = sqrt(history[rhist0]*history[rhist0] +
|
||||||
|
history[rhist1]*history[rhist1] +
|
||||||
|
history[rhist2]*history[rhist2]);
|
||||||
if (rollmag != 0.0) {
|
if (rollmag != 0.0) {
|
||||||
history[rhist0] = -1.0/k_roll*(Frcrit*fr1/fr + damp_roll*vrl1);
|
history[rhist0] = -1.0/k_roll*(Frcrit*fr1/fr + damp_roll*vrl1);
|
||||||
history[rhist1] = -1.0/k_roll*(Frcrit*fr2/fr + damp_roll*vrl2);
|
history[rhist1] = -1.0/k_roll*(Frcrit*fr2/fr + damp_roll*vrl2);
|
||||||
|
|||||||
@ -73,6 +73,7 @@ class FixWallGran : public Fix {
|
|||||||
// for granular model choices
|
// for granular model choices
|
||||||
int normal_model, damping_model;
|
int normal_model, damping_model;
|
||||||
int tangential_model, roll_model, twist_model;
|
int tangential_model, roll_model, twist_model;
|
||||||
|
int limit_damping;
|
||||||
|
|
||||||
// history flags
|
// history flags
|
||||||
int normal_history, tangential_history, roll_history, twist_history;
|
int normal_history, tangential_history, roll_history, twist_history;
|
||||||
|
|||||||
@ -181,6 +181,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
|
|||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
||||||
ccel *= polyhertz;
|
ccel *= polyhertz;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -277,7 +278,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
void PairGranHertzHistory::settings(int narg, char **arg)
|
void PairGranHertzHistory::settings(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 6) error->all(FLERR,"Illegal pair_style command");
|
if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_style command");
|
||||||
|
|
||||||
kn = utils::numeric(FLERR,arg[0],false,lmp);
|
kn = utils::numeric(FLERR,arg[0],false,lmp);
|
||||||
if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0;
|
if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0;
|
||||||
@ -295,6 +296,12 @@ void PairGranHertzHistory::settings(int narg, char **arg)
|
|||||||
xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
|
xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
|
||||||
error->all(FLERR,"Illegal pair_style command");
|
error->all(FLERR,"Illegal pair_style command");
|
||||||
|
|
||||||
|
limit_damping = 0;
|
||||||
|
if (narg == 7) {
|
||||||
|
if (strcmp(arg[6], "limit_damping") == 0) limit_damping = 1;
|
||||||
|
else error->all(FLERR,"Illegal pair_style command");
|
||||||
|
}
|
||||||
|
|
||||||
// convert Kn and Kt from pressure units to force/distance^2
|
// convert Kn and Kt from pressure units to force/distance^2
|
||||||
|
|
||||||
kn /= force->nktv2p;
|
kn /= force->nktv2p;
|
||||||
@ -388,6 +395,7 @@ double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
|
|||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
||||||
ccel *= polyhertz;
|
ccel *= polyhertz;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -158,6 +158,7 @@ void PairGranHooke::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -299,6 +300,7 @@ double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -237,6 +237,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
@ -356,7 +357,7 @@ void PairGranHookeHistory::allocate()
|
|||||||
|
|
||||||
void PairGranHookeHistory::settings(int narg, char **arg)
|
void PairGranHookeHistory::settings(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 6) error->all(FLERR,"Illegal pair_style command");
|
if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_style command");
|
||||||
|
|
||||||
kn = utils::numeric(FLERR,arg[0],false,lmp);
|
kn = utils::numeric(FLERR,arg[0],false,lmp);
|
||||||
if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0;
|
if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0;
|
||||||
@ -370,6 +371,12 @@ void PairGranHookeHistory::settings(int narg, char **arg)
|
|||||||
dampflag = utils::inumeric(FLERR,arg[5],false,lmp);
|
dampflag = utils::inumeric(FLERR,arg[5],false,lmp);
|
||||||
if (dampflag == 0) gammat = 0.0;
|
if (dampflag == 0) gammat = 0.0;
|
||||||
|
|
||||||
|
limit_damping = 0;
|
||||||
|
if (narg == 7) {
|
||||||
|
if (strcmp(arg[6], "limit_damping") == 0) limit_damping = 1;
|
||||||
|
else error->all(FLERR,"Illegal pair_style command");
|
||||||
|
}
|
||||||
|
|
||||||
if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
|
if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
|
||||||
xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
|
xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
|
||||||
error->all(FLERR,"Illegal pair_style command");
|
error->all(FLERR,"Illegal pair_style command");
|
||||||
@ -686,6 +693,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if(limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -49,6 +49,7 @@ class PairGranHookeHistory : public Pair {
|
|||||||
double dt;
|
double dt;
|
||||||
int freeze_group_bit;
|
int freeze_group_bit;
|
||||||
int history;
|
int history;
|
||||||
|
int limit_damping;
|
||||||
|
|
||||||
int neighprev;
|
int neighprev;
|
||||||
double *onerad_dynamic,*onerad_frozen;
|
double *onerad_dynamic,*onerad_frozen;
|
||||||
|
|||||||
@ -81,6 +81,8 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
|
|||||||
maxrad_dynamic = nullptr;
|
maxrad_dynamic = nullptr;
|
||||||
maxrad_frozen = nullptr;
|
maxrad_frozen = nullptr;
|
||||||
|
|
||||||
|
limit_damping = nullptr;
|
||||||
|
|
||||||
history_transfer_factors = nullptr;
|
history_transfer_factors = nullptr;
|
||||||
|
|
||||||
dt = update->dt;
|
dt = update->dt;
|
||||||
@ -130,6 +132,7 @@ PairGranular::~PairGranular()
|
|||||||
memory->destroy(tangential_model);
|
memory->destroy(tangential_model);
|
||||||
memory->destroy(roll_model);
|
memory->destroy(roll_model);
|
||||||
memory->destroy(twist_model);
|
memory->destroy(twist_model);
|
||||||
|
memory->destroy(limit_damping);
|
||||||
|
|
||||||
delete [] onerad_dynamic;
|
delete [] onerad_dynamic;
|
||||||
delete [] onerad_frozen;
|
delete [] onerad_frozen;
|
||||||
@ -364,12 +367,13 @@ void PairGranular::compute(int eflag, int vflag)
|
|||||||
damp_normal = a*meff;
|
damp_normal = a*meff;
|
||||||
} else if (damping_model[itype][jtype] == TSUJI) {
|
} else if (damping_model[itype][jtype] == TSUJI) {
|
||||||
damp_normal = sqrt(meff*knfac);
|
damp_normal = sqrt(meff*knfac);
|
||||||
}
|
} else damp_normal = 0.0;
|
||||||
|
|
||||||
damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal;
|
damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal;
|
||||||
Fdamp = -damp_normal_prefactor*vnnr;
|
Fdamp = -damp_normal_prefactor*vnnr;
|
||||||
|
|
||||||
Fntot = Fne + Fdamp;
|
Fntot = Fne + Fdamp;
|
||||||
|
if (limit_damping[itype][jtype] && (Fntot < 0.0)) Fntot = 0.0;
|
||||||
|
|
||||||
//****************************************
|
//****************************************
|
||||||
// tangential force, including history effects
|
// tangential force, including history effects
|
||||||
@ -540,20 +544,17 @@ void PairGranular::compute(int eflag, int vflag)
|
|||||||
relrot1 = omega[i][0] - omega[j][0];
|
relrot1 = omega[i][0] - omega[j][0];
|
||||||
relrot2 = omega[i][1] - omega[j][1];
|
relrot2 = omega[i][1] - omega[j][1];
|
||||||
relrot3 = omega[i][2] - omega[j][2];
|
relrot3 = omega[i][2] - omega[j][2];
|
||||||
// rolling velocity,
|
|
||||||
// see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
|
|
||||||
// this is different from the Marshall papers,
|
|
||||||
// which use the Bagi/Kuhn formulation
|
|
||||||
// for rolling velocity (see Wang et al for why the latter is wrong)
|
|
||||||
// - 0.5*((radj-radi)/radsum)*vtr1;
|
|
||||||
// - 0.5*((radj-radi)/radsum)*vtr2;
|
|
||||||
// - 0.5*((radj-radi)/radsum)*vtr3;
|
|
||||||
}
|
}
|
||||||
//****************************************
|
//****************************************
|
||||||
// rolling resistance
|
// rolling resistance
|
||||||
//****************************************
|
//****************************************
|
||||||
|
|
||||||
if (roll_model[itype][jtype] != ROLL_NONE) {
|
if (roll_model[itype][jtype] != ROLL_NONE) {
|
||||||
|
// rolling velocity,
|
||||||
|
// see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
|
||||||
|
// this is different from the Marshall papers,
|
||||||
|
// which use the Bagi/Kuhn formulation
|
||||||
|
// for rolling velocity (see Wang et al for why the latter is wrong)
|
||||||
vrl1 = Reff*(relrot2*nz - relrot3*ny);
|
vrl1 = Reff*(relrot2*nz - relrot3*ny);
|
||||||
vrl2 = Reff*(relrot3*nx - relrot1*nz);
|
vrl2 = Reff*(relrot3*nx - relrot1*nz);
|
||||||
vrl3 = Reff*(relrot1*ny - relrot2*nx);
|
vrl3 = Reff*(relrot1*ny - relrot2*nx);
|
||||||
@ -740,6 +741,7 @@ void PairGranular::allocate()
|
|||||||
memory->create(tangential_model,n+1,n+1,"pair:tangential_model");
|
memory->create(tangential_model,n+1,n+1,"pair:tangential_model");
|
||||||
memory->create(roll_model,n+1,n+1,"pair:roll_model");
|
memory->create(roll_model,n+1,n+1,"pair:roll_model");
|
||||||
memory->create(twist_model,n+1,n+1,"pair:twist_model");
|
memory->create(twist_model,n+1,n+1,"pair:twist_model");
|
||||||
|
memory->create(limit_damping,n+1,n+1,"pair:limit_damping");
|
||||||
|
|
||||||
onerad_dynamic = new double[n+1];
|
onerad_dynamic = new double[n+1];
|
||||||
onerad_frozen = new double[n+1];
|
onerad_frozen = new double[n+1];
|
||||||
@ -793,6 +795,7 @@ void PairGranular::coeff(int narg, char **arg)
|
|||||||
roll_model_one = ROLL_NONE;
|
roll_model_one = ROLL_NONE;
|
||||||
twist_model_one = TWIST_NONE;
|
twist_model_one = TWIST_NONE;
|
||||||
damping_model_one = VISCOELASTIC;
|
damping_model_one = VISCOELASTIC;
|
||||||
|
int ld_flag = 0;
|
||||||
|
|
||||||
int iarg = 2;
|
int iarg = 2;
|
||||||
while (iarg < narg) {
|
while (iarg < narg) {
|
||||||
@ -967,12 +970,15 @@ void PairGranular::coeff(int narg, char **arg)
|
|||||||
error->all(FLERR, "Illegal pair_coeff command, not enough parameters");
|
error->all(FLERR, "Illegal pair_coeff command, not enough parameters");
|
||||||
cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
cutoff_one = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||||
iarg += 2;
|
iarg += 2;
|
||||||
} else error->all(FLERR, "Illegal pair coeff command");
|
} else if (strcmp(arg[iarg], "limit_damping") == 0) {
|
||||||
|
ld_flag = 1;
|
||||||
|
iarg += 1;
|
||||||
|
} else error->all(FLERR, "Illegal pair_coeff command");
|
||||||
}
|
}
|
||||||
|
|
||||||
// error not to specify normal or tangential model
|
// error not to specify normal or tangential model
|
||||||
if ((normal_model_one < 0) || (tangential_model_one < 0))
|
if ((normal_model_one < 0) || (tangential_model_one < 0))
|
||||||
error->all(FLERR, "Illegal pair coeff command, "
|
error->all(FLERR, "Illegal pair_coeff command, "
|
||||||
"must specify normal or tangential contact model");
|
"must specify normal or tangential contact model");
|
||||||
|
|
||||||
int count = 0;
|
int count = 0;
|
||||||
@ -984,6 +990,14 @@ void PairGranular::coeff(int narg, char **arg)
|
|||||||
27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6);
|
27.467*powint(cor,4)-18.022*powint(cor,5)+4.8218*powint(cor,6);
|
||||||
} else damp = normal_coeffs_one[1];
|
} else damp = normal_coeffs_one[1];
|
||||||
|
|
||||||
|
if (ld_flag && normal_model_one == JKR)
|
||||||
|
error->all(FLERR,"Illegal pair_coeff command, "
|
||||||
|
"Cannot limit damping with JKR model");
|
||||||
|
|
||||||
|
if (ld_flag && normal_model_one == DMT)
|
||||||
|
error->all(FLERR,"Illegal pair_coeff command, "
|
||||||
|
"Cannot limit damping with DMT model");
|
||||||
|
|
||||||
for (int i = ilo; i <= ihi; i++) {
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||||
normal_model[i][j] = normal_model[j][i] = normal_model_one;
|
normal_model[i][j] = normal_model[j][i] = normal_model_one;
|
||||||
@ -1026,11 +1040,14 @@ void PairGranular::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one;
|
cutoff_type[i][j] = cutoff_type[j][i] = cutoff_one;
|
||||||
|
|
||||||
|
limit_damping[i][j] = limit_damping[j][i] = ld_flag;
|
||||||
|
|
||||||
setflag[i][j] = 1;
|
setflag[i][j] = 1;
|
||||||
count++;
|
count++;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1303,6 +1320,7 @@ void PairGranular::write_restart(FILE *fp)
|
|||||||
fwrite(&tangential_model[i][j],sizeof(int),1,fp);
|
fwrite(&tangential_model[i][j],sizeof(int),1,fp);
|
||||||
fwrite(&roll_model[i][j],sizeof(int),1,fp);
|
fwrite(&roll_model[i][j],sizeof(int),1,fp);
|
||||||
fwrite(&twist_model[i][j],sizeof(int),1,fp);
|
fwrite(&twist_model[i][j],sizeof(int),1,fp);
|
||||||
|
fwrite(&limit_damping[i][j],sizeof(int),1,fp);
|
||||||
fwrite(normal_coeffs[i][j],sizeof(double),4,fp);
|
fwrite(normal_coeffs[i][j],sizeof(double),4,fp);
|
||||||
fwrite(tangential_coeffs[i][j],sizeof(double),3,fp);
|
fwrite(tangential_coeffs[i][j],sizeof(double),3,fp);
|
||||||
fwrite(roll_coeffs[i][j],sizeof(double),3,fp);
|
fwrite(roll_coeffs[i][j],sizeof(double),3,fp);
|
||||||
@ -1333,6 +1351,7 @@ void PairGranular::read_restart(FILE *fp)
|
|||||||
utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,nullptr,error);
|
||||||
utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,nullptr,error);
|
||||||
utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,nullptr,error);
|
||||||
|
utils::sfread(FLERR,&limit_damping[i][j],sizeof(int),1,fp,nullptr,error);
|
||||||
utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error);
|
utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,nullptr,error);
|
||||||
utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error);
|
utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,nullptr,error);
|
||||||
utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error);
|
utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,nullptr,error);
|
||||||
@ -1344,6 +1363,7 @@ void PairGranular::read_restart(FILE *fp)
|
|||||||
MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world);
|
MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world);
|
||||||
MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world);
|
MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world);
|
||||||
MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world);
|
MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(&limit_damping[i][j],1,MPI_INT,0,world);
|
||||||
MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world);
|
MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world);
|
||||||
MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world);
|
MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world);
|
||||||
MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world);
|
MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world);
|
||||||
@ -1529,6 +1549,7 @@ double PairGranular::single(int i, int j, int itype, int jtype,
|
|||||||
Fdamp = -damp_normal_prefactor*vnnr;
|
Fdamp = -damp_normal_prefactor*vnnr;
|
||||||
|
|
||||||
Fntot = Fne + Fdamp;
|
Fntot = Fne + Fdamp;
|
||||||
|
if (limit_damping[itype][jtype] && (Fntot < 0.0)) Fntot = 0.0;
|
||||||
|
|
||||||
jnum = list->numneigh[i];
|
jnum = list->numneigh[i];
|
||||||
jlist = list->firstneigh[i];
|
jlist = list->firstneigh[i];
|
||||||
|
|||||||
@ -70,6 +70,7 @@ class PairGranular : public Pair {
|
|||||||
// model choices
|
// model choices
|
||||||
int **normal_model, **damping_model;
|
int **normal_model, **damping_model;
|
||||||
int **tangential_model, **roll_model, **twist_model;
|
int **tangential_model, **roll_model, **twist_model;
|
||||||
|
int **limit_damping;
|
||||||
|
|
||||||
// history flags
|
// history flags
|
||||||
int normal_history, tangential_history, roll_history, twist_history;
|
int normal_history, tangential_history, roll_history, twist_history;
|
||||||
|
|||||||
@ -392,6 +392,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
|
|||||||
|
|
||||||
F_FLOAT damp = meff*gamman*vnnr*rsqinv;
|
F_FLOAT damp = meff*gamman*vnnr*rsqinv;
|
||||||
F_FLOAT ccel = kn*(radsum-r)*rinv - damp;
|
F_FLOAT ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if(limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -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;
|
||||||
|
|||||||
@ -21,6 +21,7 @@
|
|||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "lmppython.h"
|
#include "lmppython.h"
|
||||||
#include "python_compat.h"
|
#include "python_compat.h"
|
||||||
|
#include "python_utils.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
@ -51,12 +52,12 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
}
|
}
|
||||||
|
|
||||||
// get Python function
|
// get Python function
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
PyObject *pyMain = PyImport_AddModule("__main__");
|
PyObject *pyMain = PyImport_AddModule("__main__");
|
||||||
|
|
||||||
if (!pyMain) {
|
if (!pyMain) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,"Could not initialize embedded Python");
|
error->all(FLERR,"Could not initialize embedded Python");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -64,11 +65,19 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
pFunc = PyObject_GetAttrString(pyMain, fname);
|
pFunc = PyObject_GetAttrString(pyMain, fname);
|
||||||
|
|
||||||
if (!pFunc) {
|
if (!pFunc) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,"Could not find Python function");
|
error->all(FLERR,"Could not find Python function");
|
||||||
}
|
}
|
||||||
|
|
||||||
PyGILState_Release(gstate);
|
lmpPtr = PY_VOID_POINTER(lmp);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixPythonInvoke::~FixPythonInvoke()
|
||||||
|
{
|
||||||
|
PyUtils::GIL lock;
|
||||||
|
Py_CLEAR(lmpPtr);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -82,36 +91,32 @@ int FixPythonInvoke::setmask()
|
|||||||
|
|
||||||
void FixPythonInvoke::end_of_step()
|
void FixPythonInvoke::end_of_step()
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
PyObject *ptr = PY_VOID_POINTER(lmp);
|
PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr);
|
||||||
PyObject *arglist = Py_BuildValue("(O)", ptr);
|
|
||||||
|
|
||||||
PyObject *result = PyEval_CallObject((PyObject*)pFunc, arglist);
|
if (!result) {
|
||||||
Py_DECREF(arglist);
|
PyUtils::Print_Errors();
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result)
|
|
||||||
error->all(FLERR,"Fix python/invoke end_of_step() method failed");
|
error->all(FLERR,"Fix python/invoke end_of_step() method failed");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
Py_CLEAR(result);
|
||||||
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonInvoke::post_force(int vflag)
|
void FixPythonInvoke::post_force(int vflag)
|
||||||
{
|
{
|
||||||
if (update->ntimestep % nevery != 0) return;
|
if (update->ntimestep % nevery != 0) return;
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
PyObject *ptr = PY_VOID_POINTER(lmp);
|
PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag);
|
||||||
PyObject *arglist = Py_BuildValue("(Oi)", ptr, vflag);
|
|
||||||
|
|
||||||
PyObject *result = PyEval_CallObject((PyObject*)pFunc, arglist);
|
if (!result) {
|
||||||
Py_DECREF(arglist);
|
PyUtils::Print_Errors();
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result)
|
|
||||||
error->all(FLERR,"Fix python/invoke post_force() method failed");
|
error->all(FLERR,"Fix python/invoke post_force() method failed");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
Py_CLEAR(result);
|
||||||
|
}
|
||||||
|
|||||||
@ -21,6 +21,7 @@ FixStyle(python,FixPythonInvoke)
|
|||||||
#ifndef LMP_FIX_PYTHON_INVOKE_H
|
#ifndef LMP_FIX_PYTHON_INVOKE_H
|
||||||
#define LMP_FIX_PYTHON_INVOKE_H
|
#define LMP_FIX_PYTHON_INVOKE_H
|
||||||
|
|
||||||
|
|
||||||
#include "fix.h"
|
#include "fix.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
@ -28,12 +29,13 @@ namespace LAMMPS_NS {
|
|||||||
class FixPythonInvoke : public Fix {
|
class FixPythonInvoke : public Fix {
|
||||||
public:
|
public:
|
||||||
FixPythonInvoke(class LAMMPS *, int, char **);
|
FixPythonInvoke(class LAMMPS *, int, char **);
|
||||||
virtual ~FixPythonInvoke() {}
|
virtual ~FixPythonInvoke();
|
||||||
int setmask();
|
int setmask();
|
||||||
virtual void end_of_step();
|
virtual void end_of_step();
|
||||||
virtual void post_force(int);
|
virtual void post_force(int);
|
||||||
|
|
||||||
private:
|
private:
|
||||||
|
void * lmpPtr;
|
||||||
void * pFunc;
|
void * pFunc;
|
||||||
int selected_callback;
|
int selected_callback;
|
||||||
};
|
};
|
||||||
|
|||||||
@ -21,8 +21,9 @@
|
|||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "lmppython.h"
|
#include "lmppython.h"
|
||||||
#include "python_compat.h"
|
#include "python_compat.h"
|
||||||
|
#include "python_utils.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <string>
|
||||||
#include <Python.h> // IWYU pragma: export
|
#include <Python.h> // IWYU pragma: export
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -40,7 +41,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
py_move = nullptr;
|
py_move = nullptr;
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
// add current directory to PYTHONPATH
|
// add current directory to PYTHONPATH
|
||||||
PyObject *py_path = PySys_GetObject((char *)"path");
|
PyObject *py_path = PySys_GetObject((char *)"path");
|
||||||
@ -48,70 +49,50 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
|
|
||||||
// create integrator instance
|
// create integrator instance
|
||||||
char *full_cls_name = arg[3];
|
std::string full_cls_name = arg[3];
|
||||||
char *lastpos = strrchr(full_cls_name, '.');
|
size_t lastpos = full_cls_name.rfind(".");
|
||||||
|
|
||||||
if (lastpos == nullptr) {
|
if (lastpos == std::string::npos) {
|
||||||
error->all(FLERR,"Fix python/integrate requires fully qualified class name");
|
error->all(FLERR,"Fix python/integrate requires fully qualified class name");
|
||||||
}
|
}
|
||||||
|
|
||||||
size_t module_name_length = strlen(full_cls_name) - strlen(lastpos);
|
std::string module_name = full_cls_name.substr(0, lastpos);
|
||||||
size_t cls_name_length = strlen(lastpos)-1;
|
std::string cls_name = full_cls_name.substr(lastpos+1);
|
||||||
|
|
||||||
char *module_name = new char[module_name_length+1];
|
PyObject *pModule = PyImport_ImportModule(module_name.c_str());
|
||||||
char *cls_name = new char[cls_name_length+1];
|
|
||||||
strncpy(module_name, full_cls_name, module_name_length);
|
|
||||||
module_name[module_name_length] = 0;
|
|
||||||
|
|
||||||
strcpy(cls_name, lastpos+1);
|
|
||||||
|
|
||||||
PyObject *pModule = PyImport_ImportModule(module_name);
|
|
||||||
if (!pModule) {
|
if (!pModule) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Loading python integrator module failure");
|
error->all(FLERR,"Loading python integrator module failure");
|
||||||
}
|
}
|
||||||
|
|
||||||
// create LAMMPS atom type to potential file type mapping in python class
|
// create LAMMPS atom type to potential file type mapping in python class
|
||||||
// by calling 'lammps_pair_style.map_coeff(name,type)'
|
// by calling 'lammps_pair_style.map_coeff(name,type)'
|
||||||
|
|
||||||
PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name);
|
PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name.c_str());
|
||||||
if (!py_move_type) {
|
if (!py_move_type) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find integrator class in module'");
|
error->all(FLERR,"Could not find integrator class in module'");
|
||||||
}
|
}
|
||||||
|
|
||||||
delete [] module_name;
|
|
||||||
delete [] cls_name;
|
|
||||||
|
|
||||||
PyObject *ptr = PY_VOID_POINTER(lmp);
|
PyObject *ptr = PY_VOID_POINTER(lmp);
|
||||||
PyObject *arglist = Py_BuildValue("(O)", ptr);
|
PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr);
|
||||||
PyObject *py_move_obj = PyObject_CallObject(py_move_type, arglist);
|
Py_CLEAR(ptr);
|
||||||
Py_DECREF(arglist);
|
|
||||||
|
|
||||||
if (!py_move_obj) {
|
if (!py_move_obj) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not instantiate instance of integrator class'");
|
error->all(FLERR,"Could not instantiate instance of integrator class'");
|
||||||
}
|
}
|
||||||
|
|
||||||
// check object interface
|
// check object interface
|
||||||
py_move = (void *) py_move_obj;
|
py_move = (void *) py_move_obj;
|
||||||
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixPythonMove::~FixPythonMove()
|
FixPythonMove::~FixPythonMove()
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
if (py_move) Py_DECREF((PyObject*) py_move);
|
Py_CLEAR(py_move);
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -130,122 +111,82 @@ int FixPythonMove::setmask()
|
|||||||
|
|
||||||
void FixPythonMove::init()
|
void FixPythonMove::init()
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr);
|
||||||
PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init");
|
|
||||||
if (!py_init) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move init() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'init()' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *result = PyEval_CallObject(py_init, nullptr);
|
Py_CLEAR(result);
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move init() method failed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonMove::initial_integrate(int vflag)
|
void FixPythonMove::initial_integrate(int vflag)
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag);
|
||||||
PyObject *py_initial_integrate = PyObject_GetAttrString(py_move_obj,"initial_integrate");
|
|
||||||
if (!py_initial_integrate) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move initial_integrate() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'initial_integrate' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *arglist = Py_BuildValue("(i)", vflag);
|
Py_CLEAR(result);
|
||||||
PyObject *result = PyEval_CallObject(py_initial_integrate, arglist);
|
|
||||||
Py_DECREF(arglist);
|
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move initial_integrate() "
|
|
||||||
"method failed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonMove::final_integrate()
|
void FixPythonMove::final_integrate()
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr);
|
||||||
PyObject *py_final_integrate = PyObject_GetAttrString(py_move_obj,"final_integrate");
|
|
||||||
if (!py_final_integrate) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move final_integrate() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'final_integrate' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *result = PyEval_CallObject(py_final_integrate, nullptr);
|
Py_CLEAR(result);
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move final_integrate() method "
|
|
||||||
"failed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
|
void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop);
|
||||||
PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_move_obj,"initial_integrate_respa");
|
|
||||||
if (!py_initial_integrate_respa) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move initial_integrate_respa() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'initial_integrate_respa' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *arglist = Py_BuildValue("(iii)", vflag, ilevel, iloop);
|
Py_CLEAR(result);
|
||||||
PyObject *result = PyEval_CallObject(py_initial_integrate_respa, arglist);
|
|
||||||
Py_DECREF(arglist);
|
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move initial_integrate_respa() "
|
|
||||||
"method failed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
|
void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop);
|
||||||
PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_move_obj,"final_integrate_respa");
|
|
||||||
if (!py_final_integrate_respa) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move final_integrate_respa() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'final_integrate_respa' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *arglist = Py_BuildValue("(ii)", ilevel, iloop);
|
Py_CLEAR(result);
|
||||||
PyObject *result = PyEval_CallObject(py_final_integrate_respa, arglist);
|
|
||||||
Py_DECREF(arglist);
|
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move final_integrate_respa() "
|
|
||||||
"method failed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixPythonMove::reset_dt()
|
void FixPythonMove::reset_dt()
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_move_obj = (PyObject *) py_move;
|
PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr);
|
||||||
PyObject *py_reset_dt = PyObject_GetAttrString(py_move_obj,"reset_dt");
|
|
||||||
if (!py_reset_dt) {
|
if (!result) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
error->all(FLERR,"Fix python/move reset_dt() method failed");
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'reset_dt' method'");
|
|
||||||
}
|
}
|
||||||
PyObject *result = PyEval_CallObject(py_reset_dt, nullptr);
|
Py_CLEAR(result);
|
||||||
if (!result && (comm->me == 0)) PyErr_Print();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
if (!result) error->all(FLERR,"Fix python/move reset_dt() method failed");
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -24,9 +24,10 @@
|
|||||||
#include "memory.h"
|
#include "memory.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "python_compat.h"
|
#include "python_compat.h"
|
||||||
|
#include "python_utils.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <string>
|
||||||
#include <Python.h> // IWYU pragma: export
|
#include <Python.h> // IWYU pragma: export
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -50,7 +51,7 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
|||||||
|
|
||||||
// add current directory to PYTHONPATH
|
// add current directory to PYTHONPATH
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_path = PySys_GetObject((char *)"path");
|
PyObject *py_path = PySys_GetObject((char *)"path");
|
||||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||||
|
|
||||||
@ -61,14 +62,14 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
|||||||
if (potentials_path != nullptr) {
|
if (potentials_path != nullptr) {
|
||||||
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
||||||
}
|
}
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
PairPython::~PairPython()
|
PairPython::~PairPython()
|
||||||
{
|
{
|
||||||
if (py_potential) Py_DECREF((PyObject*) py_potential);
|
PyUtils::GIL lock;
|
||||||
|
Py_CLEAR(py_potential);
|
||||||
delete[] skip_types;
|
delete[] skip_types;
|
||||||
|
|
||||||
if (allocated) {
|
if (allocated) {
|
||||||
@ -103,41 +104,31 @@ void PairPython::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
// prepare access to compute_force and compute_energy functions
|
// prepare access to compute_force and compute_energy functions
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_pair_instance = (PyObject *) py_potential;
|
PyObject *py_pair_instance = (PyObject *) py_potential;
|
||||||
PyObject *py_compute_force = PyObject_GetAttrString(py_pair_instance,"compute_force");
|
PyObject *py_compute_force = PyObject_GetAttrString(py_pair_instance,"compute_force");
|
||||||
if (!py_compute_force) {
|
if (!py_compute_force) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'compute_force' method'");
|
error->all(FLERR,"Could not find 'compute_force' method'");
|
||||||
}
|
}
|
||||||
if (!PyCallable_Check(py_compute_force)) {
|
if (!PyCallable_Check(py_compute_force)) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'compute_force' is not callable");
|
error->all(FLERR,"Python 'compute_force' is not callable");
|
||||||
}
|
}
|
||||||
|
|
||||||
PyObject *py_compute_energy = PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
PyObject *py_compute_energy = PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
||||||
if (!py_compute_energy) {
|
if (!py_compute_energy) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'compute_energy' method'");
|
error->all(FLERR,"Could not find 'compute_energy' method'");
|
||||||
}
|
}
|
||||||
if (!PyCallable_Check(py_compute_energy)) {
|
if (!PyCallable_Check(py_compute_energy)) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'compute_energy' is not callable");
|
error->all(FLERR,"Python 'compute_energy' is not callable");
|
||||||
}
|
}
|
||||||
|
|
||||||
PyObject *py_compute_args = PyTuple_New(3);
|
PyObject *py_compute_args = PyTuple_New(3);
|
||||||
if (!py_compute_args) {
|
if (!py_compute_args) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -179,13 +170,11 @@ void PairPython::compute(int eflag, int vflag)
|
|||||||
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
||||||
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
||||||
if (!py_value) {
|
if (!py_value) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Calling 'compute_force' function failed");
|
error->all(FLERR,"Calling 'compute_force' function failed");
|
||||||
}
|
}
|
||||||
fpair = factor_lj*PyFloat_AsDouble(py_value);
|
fpair = factor_lj*PyFloat_AsDouble(py_value);
|
||||||
Py_DECREF(py_value);
|
Py_CLEAR(py_value);
|
||||||
|
|
||||||
f[i][0] += delx*fpair;
|
f[i][0] += delx*fpair;
|
||||||
f[i][1] += dely*fpair;
|
f[i][1] += dely*fpair;
|
||||||
@ -198,8 +187,12 @@ void PairPython::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
if (eflag) {
|
if (eflag) {
|
||||||
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
|
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
|
||||||
|
if (!py_value) {
|
||||||
|
PyUtils::Print_Errors();
|
||||||
|
error->all(FLERR,"Calling 'compute_energy' function failed");
|
||||||
|
}
|
||||||
evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
||||||
Py_DECREF(py_value);
|
Py_CLEAR(py_value);
|
||||||
} else evdwl = 0.0;
|
} else evdwl = 0.0;
|
||||||
|
|
||||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||||
@ -207,8 +200,7 @@ void PairPython::compute(int eflag, int vflag)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
Py_DECREF(py_compute_args);
|
Py_CLEAR(py_compute_args);
|
||||||
PyGILState_Release(gstate);
|
|
||||||
|
|
||||||
if (vflag_fdotr) virial_fdotr_compute();
|
if (vflag_fdotr) virial_fdotr_compute();
|
||||||
}
|
}
|
||||||
@ -261,112 +253,49 @@ void PairPython::coeff(int narg, char **arg)
|
|||||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
|
||||||
// check if python potential file exists and source it
|
// check if python potential file exists and source it
|
||||||
char * full_cls_name = arg[2];
|
std::string full_cls_name = arg[2];
|
||||||
char * lastpos = strrchr(full_cls_name, '.');
|
size_t lastpos = full_cls_name.rfind(".");
|
||||||
|
|
||||||
if (lastpos == nullptr) {
|
if (lastpos == std::string::npos) {
|
||||||
error->all(FLERR,"Python pair style requires fully qualified class name");
|
error->all(FLERR,"Python pair style requires fully qualified class name");
|
||||||
}
|
}
|
||||||
|
|
||||||
size_t module_name_length = strlen(full_cls_name) - strlen(lastpos);
|
std::string module_name = full_cls_name.substr(0, lastpos);
|
||||||
size_t cls_name_length = strlen(lastpos)-1;
|
std::string cls_name = full_cls_name.substr(lastpos+1);
|
||||||
|
|
||||||
char * module_name = new char[module_name_length+1];
|
PyUtils::GIL lock;
|
||||||
char * cls_name = new char[cls_name_length+1];
|
|
||||||
strncpy(module_name, full_cls_name, module_name_length);
|
|
||||||
module_name[module_name_length] = 0;
|
|
||||||
|
|
||||||
strcpy(cls_name, lastpos+1);
|
PyObject * pModule = PyImport_ImportModule(module_name.c_str());
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
|
||||||
|
|
||||||
PyObject * pModule = PyImport_ImportModule(module_name);
|
|
||||||
if (!pModule) {
|
if (!pModule) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Loading python pair style module failure");
|
error->all(FLERR,"Loading python pair style module failure");
|
||||||
}
|
}
|
||||||
|
|
||||||
// create LAMMPS atom type to potential file type mapping in python class
|
// create LAMMPS atom type to potential file type mapping in python class
|
||||||
// by calling 'lammps_pair_style.map_coeff(name,type)'
|
// by calling 'lammps_pair_style.map_coeff(name,type)'
|
||||||
|
|
||||||
PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name);
|
PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name.c_str());
|
||||||
if (!py_pair_type) {
|
if (!py_pair_type) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find pair style class in module'");
|
error->all(FLERR,"Could not find pair style class in module'");
|
||||||
}
|
}
|
||||||
|
|
||||||
delete [] module_name;
|
|
||||||
delete [] cls_name;
|
|
||||||
|
|
||||||
PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, nullptr);
|
PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, nullptr);
|
||||||
if (!py_pair_instance) {
|
if (!py_pair_instance) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not instantiate instance of pair style class'");
|
error->all(FLERR,"Could not instantiate instance of pair style class'");
|
||||||
}
|
}
|
||||||
|
|
||||||
py_potential = (void *) py_pair_instance;
|
py_potential = (void *) py_pair_instance;
|
||||||
|
|
||||||
PyObject *py_check_units = PyObject_GetAttrString(py_pair_instance,"check_units");
|
PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style);
|
||||||
if (!py_check_units) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'check_units' method'");
|
|
||||||
}
|
|
||||||
if (!PyCallable_Check(py_check_units)) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'check_units' is not callable");
|
|
||||||
}
|
|
||||||
PyObject *py_units_args = PyTuple_New(1);
|
|
||||||
if (!py_units_args) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not create tuple for 'check_units' function arguments");
|
|
||||||
}
|
|
||||||
|
|
||||||
PyObject *py_name = PY_STRING_FROM_STRING(update->unit_style);
|
|
||||||
PyTuple_SetItem(py_units_args,0,py_name);
|
|
||||||
PyObject *py_value = PyObject_CallObject(py_check_units,py_units_args);
|
|
||||||
if (!py_value) {
|
if (!py_value) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Calling 'check_units' function failed");
|
error->all(FLERR,"Calling 'check_units' function failed");
|
||||||
}
|
}
|
||||||
Py_DECREF(py_units_args);
|
Py_CLEAR(py_value);
|
||||||
|
|
||||||
|
|
||||||
PyObject *py_map_coeff = PyObject_GetAttrString(py_pair_instance,"map_coeff");
|
|
||||||
if (!py_map_coeff) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'map_coeff' method'");
|
|
||||||
}
|
|
||||||
if (!PyCallable_Check(py_map_coeff)) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'map_coeff' is not callable");
|
|
||||||
}
|
|
||||||
|
|
||||||
PyObject *py_map_args = PyTuple_New(2);
|
|
||||||
if (!py_map_args) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not create tuple for 'map_coeff' function arguments");
|
|
||||||
}
|
|
||||||
|
|
||||||
delete[] skip_types;
|
delete[] skip_types;
|
||||||
skip_types = new int[ntypes+1];
|
skip_types = new int[ntypes+1];
|
||||||
skip_types[0] = 1;
|
skip_types[0] = 1;
|
||||||
@ -375,25 +304,20 @@ void PairPython::coeff(int narg, char **arg)
|
|||||||
skip_types[i] = 1;
|
skip_types[i] = 1;
|
||||||
continue;
|
continue;
|
||||||
} else skip_types[i] = 0;
|
} else skip_types[i] = 0;
|
||||||
PyObject *py_type = PY_INT_FROM_LONG(i);
|
const int type = i;
|
||||||
py_name = PY_STRING_FROM_STRING(arg[2+i]);
|
const char * name = arg[2+i];
|
||||||
PyTuple_SetItem(py_map_args,0,py_name);
|
py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type);
|
||||||
PyTuple_SetItem(py_map_args,1,py_type);
|
|
||||||
py_value = PyObject_CallObject(py_map_coeff,py_map_args);
|
|
||||||
if (!py_value) {
|
if (!py_value) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Calling 'map_coeff' function failed");
|
error->all(FLERR,"Calling 'map_coeff' function failed");
|
||||||
}
|
}
|
||||||
|
Py_CLEAR(py_value);
|
||||||
|
|
||||||
for (int j = i; j <= ntypes ; j++) {
|
for (int j = i; j <= ntypes ; j++) {
|
||||||
setflag[i][j] = 1;
|
setflag[i][j] = 1;
|
||||||
cutsq[i][j] = cut_global*cut_global;
|
cutsq[i][j] = cut_global*cut_global;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
Py_DECREF(py_map_args);
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -417,76 +341,52 @@ double PairPython::single(int /* i */, int /* j */, int itype, int jtype,
|
|||||||
|
|
||||||
// prepare access to compute_force and compute_energy functions
|
// prepare access to compute_force and compute_energy functions
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *py_pair_instance = (PyObject *) py_potential;
|
PyObject *py_compute_force = (PyObject *) get_member_function("compute_force");
|
||||||
PyObject *py_compute_force
|
PyObject *py_compute_energy = (PyObject *) get_member_function("compute_energy");
|
||||||
= PyObject_GetAttrString(py_pair_instance,"compute_force");
|
PyObject *py_compute_args = Py_BuildValue("(dii)", rsq, itype, jtype);
|
||||||
if (!py_compute_force) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'compute_force' method'");
|
|
||||||
}
|
|
||||||
if (!PyCallable_Check(py_compute_force)) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'compute_force' is not callable");
|
|
||||||
}
|
|
||||||
|
|
||||||
PyObject *py_compute_energy
|
|
||||||
= PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
|
||||||
if (!py_compute_energy) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not find 'compute_energy' method'");
|
|
||||||
}
|
|
||||||
if (!PyCallable_Check(py_compute_energy)) {
|
|
||||||
PyErr_Print();
|
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Python 'compute_energy' is not callable");
|
|
||||||
}
|
|
||||||
|
|
||||||
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
|
|
||||||
PyObject *py_compute_args = PyTuple_New(3);
|
|
||||||
if (!py_compute_args) {
|
if (!py_compute_args) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
||||||
}
|
}
|
||||||
|
|
||||||
py_itype = PY_INT_FROM_LONG(itype);
|
PyObject * py_value = PyObject_CallObject(py_compute_force, py_compute_args);
|
||||||
PyTuple_SetItem(py_compute_args,1,py_itype);
|
|
||||||
py_jtype = PY_INT_FROM_LONG(jtype);
|
|
||||||
PyTuple_SetItem(py_compute_args,2,py_jtype);
|
|
||||||
py_rsq = PyFloat_FromDouble(rsq);
|
|
||||||
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
|
||||||
|
|
||||||
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
|
||||||
if (!py_value) {
|
if (!py_value) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Calling 'compute_force' function failed");
|
error->all(FLERR,"Calling 'compute_force' function failed");
|
||||||
}
|
}
|
||||||
fforce = factor_lj*PyFloat_AsDouble(py_value);
|
fforce = factor_lj*PyFloat_AsDouble(py_value);
|
||||||
Py_DECREF(py_value);
|
Py_CLEAR(py_value);
|
||||||
|
|
||||||
py_value = PyObject_CallObject(py_compute_energy, py_compute_args);
|
py_value = PyObject_CallObject(py_compute_energy, py_compute_args);
|
||||||
if (!py_value) {
|
if (!py_value) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyErr_Clear();
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Calling 'compute_energy' function failed");
|
error->all(FLERR,"Calling 'compute_energy' function failed");
|
||||||
}
|
}
|
||||||
double evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
double evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
||||||
Py_DECREF(py_value);
|
|
||||||
|
|
||||||
Py_DECREF(py_compute_args);
|
Py_CLEAR(py_value);
|
||||||
PyGILState_Release(gstate);
|
Py_CLEAR(py_compute_args);
|
||||||
|
|
||||||
return evdwl;
|
return evdwl;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void * PairPython::get_member_function(const char * name)
|
||||||
|
{
|
||||||
|
PyUtils::GIL lock;
|
||||||
|
PyObject *py_pair_instance = (PyObject *) py_potential;
|
||||||
|
PyObject * py_mfunc = PyObject_GetAttrString(py_pair_instance, name);
|
||||||
|
if (!py_mfunc) {
|
||||||
|
PyUtils::Print_Errors();
|
||||||
|
error->all(FLERR, fmt::format("Could not find '{}' method'", name));
|
||||||
|
}
|
||||||
|
if (!PyCallable_Check(py_mfunc)) {
|
||||||
|
PyUtils::Print_Errors();
|
||||||
|
error->all(FLERR, fmt::format("Python '{}' is not callable", name));
|
||||||
|
}
|
||||||
|
return py_mfunc;
|
||||||
|
}
|
||||||
|
|||||||
@ -50,6 +50,7 @@ class PairPython : public Pair {
|
|||||||
int * skip_types;
|
int * skip_types;
|
||||||
|
|
||||||
virtual void allocate();
|
virtual void allocate();
|
||||||
|
void * get_member_function(const char *);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -21,6 +21,7 @@
|
|||||||
#include "input.h"
|
#include "input.h"
|
||||||
#include "memory.h"
|
#include "memory.h"
|
||||||
#include "python_compat.h"
|
#include "python_compat.h"
|
||||||
|
#include "python_utils.h"
|
||||||
#include "variable.h"
|
#include "variable.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
@ -91,13 +92,12 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
}
|
}
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
PyObject *pModule = PyImport_AddModule("__main__");
|
PyObject *pModule = PyImport_AddModule("__main__");
|
||||||
if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
|
if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
|
||||||
|
|
||||||
pyMain = (void *) pModule;
|
pyMain = (void *) pModule;
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -106,24 +106,20 @@ PythonImpl::~PythonImpl()
|
|||||||
{
|
{
|
||||||
if (pyMain) {
|
if (pyMain) {
|
||||||
// clean up
|
// clean up
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
for (int i = 0; i < nfunc; i++) {
|
for (int i = 0; i < nfunc; i++) {
|
||||||
delete [] pfuncs[i].name;
|
delete [] pfuncs[i].name;
|
||||||
deallocate(i);
|
deallocate(i);
|
||||||
PyObject *pFunc = (PyObject *) pfuncs[i].pFunc;
|
Py_CLEAR(pfuncs[i].pFunc);
|
||||||
Py_XDECREF(pFunc);
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// shutdown Python interpreter
|
// shutdown Python interpreter
|
||||||
|
|
||||||
if (!external_interpreter) {
|
if (!external_interpreter) {
|
||||||
|
PyGILState_Ensure();
|
||||||
Py_Finalize();
|
Py_Finalize();
|
||||||
}
|
}
|
||||||
else {
|
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
memory->sfree(pfuncs);
|
memory->sfree(pfuncs);
|
||||||
}
|
}
|
||||||
@ -228,7 +224,7 @@ void PythonImpl::command(int narg, char **arg)
|
|||||||
|
|
||||||
int ifunc = create_entry(arg[0]);
|
int ifunc = create_entry(arg[0]);
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
|
|
||||||
// send Python code to Python interpreter
|
// send Python code to Python interpreter
|
||||||
// file: read the file via PyRun_SimpleFile()
|
// file: read the file via PyRun_SimpleFile()
|
||||||
@ -239,14 +235,14 @@ void PythonImpl::command(int narg, char **arg)
|
|||||||
FILE *fp = fopen(pyfile,"r");
|
FILE *fp = fopen(pyfile,"r");
|
||||||
|
|
||||||
if (fp == nullptr) {
|
if (fp == nullptr) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,"Could not open Python file");
|
error->all(FLERR,"Could not open Python file");
|
||||||
}
|
}
|
||||||
|
|
||||||
int err = PyRun_SimpleFile(fp,pyfile);
|
int err = PyRun_SimpleFile(fp,pyfile);
|
||||||
|
|
||||||
if (err) {
|
if (err) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,"Could not process Python file");
|
error->all(FLERR,"Could not process Python file");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -255,7 +251,7 @@ void PythonImpl::command(int narg, char **arg)
|
|||||||
int err = PyRun_SimpleString(herestr);
|
int err = PyRun_SimpleString(herestr);
|
||||||
|
|
||||||
if (err) {
|
if (err) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,"Could not process Python string");
|
error->all(FLERR,"Could not process Python string");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -266,13 +262,13 @@ void PythonImpl::command(int narg, char **arg)
|
|||||||
PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name);
|
PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name);
|
||||||
|
|
||||||
if (!pFunc) {
|
if (!pFunc) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,fmt::format("Could not find Python function {}",
|
error->all(FLERR,fmt::format("Could not find Python function {}",
|
||||||
pfuncs[ifunc].name));
|
pfuncs[ifunc].name));
|
||||||
}
|
}
|
||||||
|
|
||||||
if (!PyCallable_Check(pFunc)) {
|
if (!PyCallable_Check(pFunc)) {
|
||||||
PyGILState_Release(gstate);
|
PyUtils::Print_Errors();
|
||||||
error->all(FLERR,fmt::format("Python function {} is not callable",
|
error->all(FLERR,fmt::format("Python function {} is not callable",
|
||||||
pfuncs[ifunc].name));
|
pfuncs[ifunc].name));
|
||||||
}
|
}
|
||||||
@ -284,14 +280,13 @@ void PythonImpl::command(int narg, char **arg)
|
|||||||
delete [] istr;
|
delete [] istr;
|
||||||
delete [] format;
|
delete [] format;
|
||||||
delete [] pyfile;
|
delete [] pyfile;
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ------------------------------------------------------------------ */
|
/* ------------------------------------------------------------------ */
|
||||||
|
|
||||||
void PythonImpl::invoke_function(int ifunc, char *result)
|
void PythonImpl::invoke_function(int ifunc, char *result)
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
PyObject *pValue;
|
PyObject *pValue;
|
||||||
char *str;
|
char *str;
|
||||||
|
|
||||||
@ -303,7 +298,6 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
PyObject *pArgs = PyTuple_New(ninput);
|
PyObject *pArgs = PyTuple_New(ninput);
|
||||||
|
|
||||||
if (!pArgs) {
|
if (!pArgs) {
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not create Python function arguments");
|
error->all(FLERR,"Could not create Python function arguments");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -314,7 +308,6 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
||||||
|
|
||||||
if (!str) {
|
if (!str) {
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not evaluate Python function input variable");
|
error->all(FLERR,"Could not evaluate Python function input variable");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -327,7 +320,6 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
||||||
|
|
||||||
if (!str) {
|
if (!str) {
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not evaluate Python function input variable");
|
error->all(FLERR,"Could not evaluate Python function input variable");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -339,7 +331,6 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
if (pfuncs[ifunc].ivarflag[i]) {
|
if (pfuncs[ifunc].ivarflag[i]) {
|
||||||
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
|
||||||
if (!str) {
|
if (!str) {
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Could not evaluate Python function input variable");
|
error->all(FLERR,"Could not evaluate Python function input variable");
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -350,7 +341,6 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
} else if (itype == PTR) {
|
} else if (itype == PTR) {
|
||||||
pValue = PY_VOID_POINTER(lmp);
|
pValue = PY_VOID_POINTER(lmp);
|
||||||
} else {
|
} else {
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->all(FLERR,"Unsupported variable type");
|
error->all(FLERR,"Unsupported variable type");
|
||||||
}
|
}
|
||||||
PyTuple_SetItem(pArgs,i,pValue);
|
PyTuple_SetItem(pArgs,i,pValue);
|
||||||
@ -360,15 +350,13 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
// error check with one() since only some procs may fail
|
// error check with one() since only some procs may fail
|
||||||
|
|
||||||
pValue = PyObject_CallObject(pFunc,pArgs);
|
pValue = PyObject_CallObject(pFunc,pArgs);
|
||||||
|
Py_CLEAR(pArgs);
|
||||||
|
|
||||||
if (!pValue) {
|
if (!pValue) {
|
||||||
PyErr_Print();
|
PyUtils::Print_Errors();
|
||||||
PyGILState_Release(gstate);
|
|
||||||
error->one(FLERR,"Python function evaluation failed");
|
error->one(FLERR,"Python function evaluation failed");
|
||||||
}
|
}
|
||||||
|
|
||||||
Py_DECREF(pArgs);
|
|
||||||
|
|
||||||
// function returned a value
|
// function returned a value
|
||||||
// assign it to result string stored by python-style variable
|
// assign it to result string stored by python-style variable
|
||||||
// or if user specified a length, assign it to longstr
|
// or if user specified a length, assign it to longstr
|
||||||
@ -385,10 +373,8 @@ void PythonImpl::invoke_function(int ifunc, char *result)
|
|||||||
strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
|
strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
|
||||||
else strncpy(result,pystr,VALUELENGTH-1);
|
else strncpy(result,pystr,VALUELENGTH-1);
|
||||||
}
|
}
|
||||||
Py_DECREF(pValue);
|
|
||||||
}
|
}
|
||||||
|
Py_CLEAR(pValue);
|
||||||
PyGILState_Release(gstate);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ------------------------------------------------------------------ */
|
/* ------------------------------------------------------------------ */
|
||||||
@ -523,11 +509,8 @@ int PythonImpl::create_entry(char *name)
|
|||||||
|
|
||||||
int PythonImpl::execute_string(char *cmd)
|
int PythonImpl::execute_string(char *cmd)
|
||||||
{
|
{
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
int err = PyRun_SimpleString(cmd);
|
return PyRun_SimpleString(cmd);
|
||||||
PyGILState_Release(gstate);
|
|
||||||
|
|
||||||
return err;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -537,9 +520,8 @@ int PythonImpl::execute_file(char *fname)
|
|||||||
FILE *fp = fopen(fname,"r");
|
FILE *fp = fopen(fname,"r");
|
||||||
if (fp == nullptr) return -1;
|
if (fp == nullptr) return -1;
|
||||||
|
|
||||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
PyUtils::GIL lock;
|
||||||
int err = PyRun_SimpleFile(fp,fname);
|
int err = PyRun_SimpleFile(fp,fname);
|
||||||
PyGILState_Release(gstate);
|
|
||||||
|
|
||||||
if (fp) fclose(fp);
|
if (fp) fclose(fp);
|
||||||
return err;
|
return err;
|
||||||
|
|||||||
42
src/PYTHON/python_utils.h
Normal file
42
src/PYTHON/python_utils.h
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifndef LMP_PYTHON_UTILS_H
|
||||||
|
#define LMP_PYTHON_UTILS_H
|
||||||
|
|
||||||
|
#include <Python.h>
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
namespace PyUtils {
|
||||||
|
|
||||||
|
class GIL {
|
||||||
|
PyGILState_STATE gstate;
|
||||||
|
public:
|
||||||
|
GIL() : gstate(PyGILState_Ensure()) {
|
||||||
|
}
|
||||||
|
~GIL() {
|
||||||
|
PyGILState_Release(gstate);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
static void Print_Errors() {
|
||||||
|
PyErr_Print();
|
||||||
|
PyErr_Clear();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
@ -234,8 +234,6 @@ void FixRigidNH::init()
|
|||||||
}
|
}
|
||||||
|
|
||||||
g_f = nf_t + nf_r;
|
g_f = nf_t + nf_r;
|
||||||
onednft = 1.0 + (double)(dimension) / (double)g_f;
|
|
||||||
onednfr = (double) (dimension) / (double)g_f;
|
|
||||||
|
|
||||||
// see Table 1 in Kamberaj et al
|
// see Table 1 in Kamberaj et al
|
||||||
|
|
||||||
@ -719,6 +717,8 @@ void FixRigidNH::final_integrate()
|
|||||||
|
|
||||||
void FixRigidNH::nhc_temp_integrate()
|
void FixRigidNH::nhc_temp_integrate()
|
||||||
{
|
{
|
||||||
|
if (g_f == 0) return;
|
||||||
|
|
||||||
int i,j,k;
|
int i,j,k;
|
||||||
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
|
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
|
||||||
|
|
||||||
@ -1063,6 +1063,8 @@ void FixRigidNH::compute_press_target()
|
|||||||
|
|
||||||
void FixRigidNH::nh_epsilon_dot()
|
void FixRigidNH::nh_epsilon_dot()
|
||||||
{
|
{
|
||||||
|
if (g_f == 0) return;
|
||||||
|
|
||||||
int i;
|
int i;
|
||||||
double volume,scale,f_epsilon;
|
double volume,scale,f_epsilon;
|
||||||
|
|
||||||
|
|||||||
@ -38,8 +38,6 @@ class FixRigidNH : public FixRigid {
|
|||||||
double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors
|
double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors
|
||||||
|
|
||||||
int nf_t,nf_r; // trans/rot degrees of freedom
|
int nf_t,nf_r; // trans/rot degrees of freedom
|
||||||
double onednft,onednfr; // factors 1 + dimension/trans(rot)
|
|
||||||
// degrees of freedom
|
|
||||||
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
|
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
|
||||||
double *q_t,*q_r; // trans/rot thermostat masses
|
double *q_t,*q_r; // trans/rot thermostat masses
|
||||||
double *eta_t,*eta_r; // trans/rot thermostat positions
|
double *eta_t,*eta_r; // trans/rot thermostat positions
|
||||||
|
|||||||
@ -754,6 +754,8 @@ void FixRigidNHSmall::final_integrate()
|
|||||||
|
|
||||||
void FixRigidNHSmall::nhc_temp_integrate()
|
void FixRigidNHSmall::nhc_temp_integrate()
|
||||||
{
|
{
|
||||||
|
if (g_f == 0) return;
|
||||||
|
|
||||||
int i,j,k;
|
int i,j,k;
|
||||||
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
|
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
|
||||||
|
|
||||||
@ -1148,6 +1150,8 @@ void FixRigidNHSmall::compute_press_target()
|
|||||||
|
|
||||||
void FixRigidNHSmall::nh_epsilon_dot()
|
void FixRigidNHSmall::nh_epsilon_dot()
|
||||||
{
|
{
|
||||||
|
if (g_f == 0) return;
|
||||||
|
|
||||||
int i;
|
int i;
|
||||||
double volume,scale,f_epsilon;
|
double volume,scale,f_epsilon;
|
||||||
|
|
||||||
@ -1204,8 +1208,6 @@ void FixRigidNHSmall::compute_dof()
|
|||||||
nf_r = nfall[1];
|
nf_r = nfall[1];
|
||||||
|
|
||||||
g_f = nf_t + nf_r;
|
g_f = nf_t + nf_r;
|
||||||
onednft = 1.0 + (double)(dimension) / (double)g_f;
|
|
||||||
onednfr = (double) (dimension) / (double)g_f;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -1367,19 +1369,6 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
|
|||||||
return FixRigidSmall::modify_param(narg,arg);
|
return FixRigidSmall::modify_param(narg,arg);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
disallow using fix rigid/n??/small fixes with fix deposit
|
|
||||||
we would need custom functionality to update data structures
|
|
||||||
used by all fixes derived from this class but not fix rigid/small
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixRigidNHSmall::set_molecule(int, tagint, int,
|
|
||||||
double *, double *, double *)
|
|
||||||
{
|
|
||||||
error->all(FLERR,fmt::format("Molecule update not (yet) implemented for "
|
|
||||||
"fix {}", style));
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixRigidNHSmall::allocate_chain()
|
void FixRigidNHSmall::allocate_chain()
|
||||||
|
|||||||
@ -38,7 +38,6 @@ class FixRigidNHSmall : public FixRigidSmall {
|
|||||||
|
|
||||||
int dimension; // # of dimensions
|
int dimension; // # of dimensions
|
||||||
int nf_t,nf_r; // trans/rot degrees of freedom
|
int nf_t,nf_r; // trans/rot degrees of freedom
|
||||||
double onednft,onednfr; // factors 1 + dimension/trans(rot) degrees of freedom
|
|
||||||
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
|
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
|
||||||
double *q_t,*q_r; // trans/rot thermostat masses
|
double *q_t,*q_r; // trans/rot thermostat masses
|
||||||
double *eta_t,*eta_r; // trans/rot thermostat positions
|
double *eta_t,*eta_r; // trans/rot thermostat positions
|
||||||
@ -80,7 +79,6 @@ class FixRigidNHSmall : public FixRigidSmall {
|
|||||||
void nh_epsilon_dot();
|
void nh_epsilon_dot();
|
||||||
void compute_dof();
|
void compute_dof();
|
||||||
|
|
||||||
void set_molecule(int, tagint, int, double *, double *, double *);
|
|
||||||
void allocate_chain();
|
void allocate_chain();
|
||||||
void allocate_order();
|
void allocate_order();
|
||||||
void deallocate_chain();
|
void deallocate_chain();
|
||||||
|
|||||||
@ -224,6 +224,7 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
|
||||||
ccel *= polyhertz;
|
ccel *= polyhertz;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -223,6 +223,7 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -197,6 +197,7 @@ void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||||||
|
|
||||||
damp = meff*gamman*vnnr*rsqinv;
|
damp = meff*gamman*vnnr*rsqinv;
|
||||||
ccel = kn*(radsum-r)*rinv - damp;
|
ccel = kn*(radsum-r)*rinv - damp;
|
||||||
|
if (limit_damping && (ccel < 0.0)) ccel = 0.0;
|
||||||
|
|
||||||
// relative velocities
|
// relative velocities
|
||||||
|
|
||||||
|
|||||||
@ -318,7 +318,6 @@ void PairQUIP::init_style()
|
|||||||
|
|
||||||
// Initialise neighbor list
|
// Initialise neighbor list
|
||||||
int irequest_full = neighbor->request(this);
|
int irequest_full = neighbor->request(this);
|
||||||
neighbor->requests[irequest_full]->id = 1;
|
|
||||||
neighbor->requests[irequest_full]->half = 0;
|
neighbor->requests[irequest_full]->half = 0;
|
||||||
neighbor->requests[irequest_full]->full = 1;
|
neighbor->requests[irequest_full]->full = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -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;
|
||||||
@ -115,10 +112,10 @@ 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;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -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
|
||||||
|
|||||||
@ -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) {
|
||||||
@ -265,16 +266,15 @@ 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;
|
||||||
|
|||||||
@ -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);
|
||||||
@ -266,16 +268,15 @@ 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;
|
||||||
|
|||||||
129
src/library.cpp
129
src/library.cpp
@ -1615,7 +1615,7 @@ lists the available options.
|
|||||||
* \return pointer (cast to ``void *``) to the location of the
|
* \return pointer (cast to ``void *``) to the location of the
|
||||||
* requested data or ``NULL`` if not found. */
|
* requested data or ``NULL`` if not found. */
|
||||||
|
|
||||||
void *lammps_extract_compute(void *handle, char *id, int style, int type)
|
void *lammps_extract_compute(void *handle, const char *id, int style, int type)
|
||||||
{
|
{
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
|
|
||||||
@ -1801,7 +1801,7 @@ The following table lists the available options.
|
|||||||
* \return pointer (cast to ``void *``) to the location of the
|
* \return pointer (cast to ``void *``) to the location of the
|
||||||
* requested data or ``NULL`` if not found. */
|
* requested data or ``NULL`` if not found. */
|
||||||
|
|
||||||
void *lammps_extract_fix(void *handle, char *id, int style, int type,
|
void *lammps_extract_fix(void *handle, const char *id, int style, int type,
|
||||||
int nrow, int ncol)
|
int nrow, int ncol)
|
||||||
{
|
{
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
@ -3822,8 +3822,8 @@ X(1),Y(1),Z(1),X(2),Y(2),Z(2),...,X(N),Y(N),Z(N).
|
|||||||
* \return number of atoms created on success;
|
* \return number of atoms created on success;
|
||||||
-1 on failure (no box, no atom IDs, etc.) */
|
-1 on failure (no box, no atom IDs, etc.) */
|
||||||
|
|
||||||
int lammps_create_atoms(void *handle, int n, tagint *id, int *type,
|
int lammps_create_atoms(void *handle, int n, const tagint *id, const int *type,
|
||||||
double *x, double *v, imageint *image,
|
const double *x, const double *v, const imageint *image,
|
||||||
int bexpand)
|
int bexpand)
|
||||||
{
|
{
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
@ -3859,13 +3859,17 @@ int lammps_create_atoms(void *handle, int n, tagint *id, int *type,
|
|||||||
|
|
||||||
int nlocal_prev = nlocal;
|
int nlocal_prev = nlocal;
|
||||||
double xdata[3];
|
double xdata[3];
|
||||||
|
imageint idata, *img;
|
||||||
|
|
||||||
for (int i = 0; i < n; i++) {
|
for (int i = 0; i < n; i++) {
|
||||||
xdata[0] = x[3*i];
|
xdata[0] = x[3*i];
|
||||||
xdata[1] = x[3*i+1];
|
xdata[1] = x[3*i+1];
|
||||||
xdata[2] = x[3*i+2];
|
xdata[2] = x[3*i+2];
|
||||||
imageint * img = image ? image + i : nullptr;
|
if (image) {
|
||||||
tagint tag = id ? id[i] : 0;
|
idata = image[i];
|
||||||
|
img = &idata;
|
||||||
|
} else img = nullptr;
|
||||||
|
const tagint tag = id ? id[i] : 0;
|
||||||
|
|
||||||
// create atom only on MPI rank that would own it
|
// create atom only on MPI rank that would own it
|
||||||
|
|
||||||
@ -3917,28 +3921,33 @@ int lammps_create_atoms(void *handle, int n, tagint *id, int *type,
|
|||||||
// Library functions for accessing neighbor lists
|
// Library functions for accessing neighbor lists
|
||||||
// ----------------------------------------------------------------------
|
// ----------------------------------------------------------------------
|
||||||
|
|
||||||
/** Find neighbor list index of pair style neighbor list
|
/** Find index of a neighbor list requested by a pair style
|
||||||
*
|
*
|
||||||
* Try finding pair instance that matches style. If exact is set, the pair must
|
* This function determines which of the available neighbor lists for
|
||||||
* match style exactly. If exact is 0, style must only be contained. If pair is
|
* pair styles matches the given conditions. It first matches the style
|
||||||
* of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
|
* name. If exact is 1 the name must match exactly, if exact is 0, a
|
||||||
|
* regular expression or sub-string match is done. If the pair style is
|
||||||
|
* hybrid or hybrid/overlay the style is matched against the sub styles
|
||||||
|
* instead.
|
||||||
|
* If a the same pair style is used multiple times as a sub-style, the
|
||||||
|
* nsub argument must be > 0 and represents the nth instance of the sub-style
|
||||||
|
* (same as for the pair_coeff command, for example). In that case
|
||||||
|
* nsub=0 will not produce a match and this function will return -1.
|
||||||
*
|
*
|
||||||
* Once the pair instance has been identified, multiple neighbor list requests
|
* The final condition to be checked is the request ID (reqid). This
|
||||||
* may be found. Every neighbor list is uniquely identified by its request
|
* will normally be 0, but some pair styles request multiple neighbor
|
||||||
* index. Thus, providing this request index ensures that the correct neighbor
|
* lists and set the request ID to a value > 0.
|
||||||
* list index is returned.
|
|
||||||
*
|
*
|
||||||
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
||||||
* \param style String used to search for pair style instance
|
* \param style String used to search for pair style instance
|
||||||
* \param exact Flag to control whether style should match exactly or only
|
* \param exact Flag to control whether style should match exactly or only
|
||||||
* must be contained in pair style name
|
* a regular expression / sub-string match is applied.
|
||||||
* \param nsub match nsub-th hybrid sub-style
|
* \param nsub match nsub-th hybrid sub-style instance of the same style
|
||||||
* \param request request index that specifies which neighbor list should be
|
* \param reqid request id to identify neighbor list in case there are
|
||||||
* returned, in case there are multiple neighbor lists requests
|
* multiple requests from the same pair style instance
|
||||||
* for the found pair style
|
|
||||||
* \return return neighbor list index if found, otherwise -1 */
|
* \return return neighbor list index if found, otherwise -1 */
|
||||||
|
|
||||||
int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub, int request) {
|
int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int nsub, int reqid) {
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
Pair *pair = lmp->force->pair_match(style, exact, nsub);
|
Pair *pair = lmp->force->pair_match(style, exact, nsub);
|
||||||
|
|
||||||
@ -3946,11 +3955,9 @@ int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub,
|
|||||||
// find neigh list
|
// find neigh list
|
||||||
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
||||||
NeighList *list = lmp->neighbor->lists[i];
|
NeighList *list = lmp->neighbor->lists[i];
|
||||||
if (list->requestor_type != NeighList::PAIR || pair != list->requestor) continue;
|
if ( (list->requestor_type == NeighList::PAIR)
|
||||||
|
&& (pair == list->requestor)
|
||||||
if (list->index == request) {
|
&& (list->id == reqid) ) return i;
|
||||||
return i;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
return -1;
|
return -1;
|
||||||
@ -3958,74 +3965,60 @@ int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub,
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
/** Find neighbor list index of fix neighbor list
|
/** Find index of a neighbor list requested by a fix
|
||||||
|
*
|
||||||
|
* The neighbor list request from a fix is identified by the fix ID and
|
||||||
|
* the request ID. The request ID is typically 0, but will be > 0 in
|
||||||
|
* case a fix has multiple neighbor list requests.
|
||||||
*
|
*
|
||||||
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
||||||
* \param id Identifier of fix instance
|
* \param id Identifier of fix instance
|
||||||
* \param request request index that specifies which request should be returned,
|
* \param reqid request id to identify neighbor list in case there are
|
||||||
* in case there are multiple neighbor lists for this fix
|
* multiple requests from the same fix
|
||||||
* \return return neighbor list index if found, otherwise -1 */
|
* \return return neighbor list index if found, otherwise -1 */
|
||||||
|
|
||||||
int lammps_find_fix_neighlist(void* handle, char *id, int request) {
|
int lammps_find_fix_neighlist(void *handle, const char *id, int reqid) {
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
Fix* fix = nullptr;
|
const int ifix = lmp->modify->find_fix(id);
|
||||||
const int nfix = lmp->modify->nfix;
|
if (ifix < 0) return -1;
|
||||||
|
|
||||||
// find fix with name
|
Fix *fix = lmp->modify->fix[ifix];
|
||||||
for (int ifix = 0; ifix < nfix; ifix++) {
|
|
||||||
if (strcmp(lmp->modify->fix[ifix]->id, id) == 0) {
|
|
||||||
fix = lmp->modify->fix[ifix];
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (fix != nullptr) {
|
|
||||||
// find neigh list
|
// find neigh list
|
||||||
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
||||||
NeighList *list = lmp->neighbor->lists[i];
|
NeighList *list = lmp->neighbor->lists[i];
|
||||||
if (list->requestor_type != NeighList::FIX || fix != list->requestor) continue;
|
if ( (list->requestor_type == NeighList::FIX)
|
||||||
|
&& (fix == list->requestor)
|
||||||
if (list->index == request) {
|
&& (list->id == reqid) ) return i;
|
||||||
return i;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
return -1;
|
return -1;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
/** Find neighbor list index of compute neighbor list
|
/** Find index of a neighbor list requested by a compute
|
||||||
|
*
|
||||||
|
* The neighbor list request from a compute is identified by the compute
|
||||||
|
* ID and the request ID. The request ID is typically 0, but will be
|
||||||
|
* > 0 in case a compute has multiple neighbor list requests.
|
||||||
*
|
*
|
||||||
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
|
||||||
* \param id Identifier of fix instance
|
* \param id Identifier of compute instance
|
||||||
* \param request request index that specifies which request should be returned,
|
* \param reqid request id to identify neighbor list in case there are
|
||||||
* in case there are multiple neighbor lists for this fix
|
* multiple requests from the same compute
|
||||||
* \return return neighbor list index if found, otherwise -1 */
|
* \return return neighbor list index if found, otherwise -1 */
|
||||||
|
|
||||||
int lammps_find_compute_neighlist(void* handle, char *id, int request) {
|
int lammps_find_compute_neighlist(void* handle, const char *id, int reqid) {
|
||||||
LAMMPS *lmp = (LAMMPS *) handle;
|
LAMMPS *lmp = (LAMMPS *) handle;
|
||||||
Compute* compute = nullptr;
|
const int icompute = lmp->modify->find_compute(id);
|
||||||
const int ncompute = lmp->modify->ncompute;
|
if (icompute < 0) return -1;
|
||||||
|
|
||||||
// find compute with name
|
Compute *compute = lmp->modify->compute[icompute];
|
||||||
for (int icompute = 0; icompute < ncompute; icompute++) {
|
|
||||||
if (strcmp(lmp->modify->compute[icompute]->id, id) == 0) {
|
|
||||||
compute = lmp->modify->compute[icompute];
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (compute != nullptr) {
|
|
||||||
// find neigh list
|
// find neigh list
|
||||||
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
for (int i = 0; i < lmp->neighbor->nlist; i++) {
|
||||||
NeighList * list = lmp->neighbor->lists[i];
|
NeighList * list = lmp->neighbor->lists[i];
|
||||||
if (list->requestor_type != NeighList::COMPUTE || compute != list->requestor) continue;
|
if ( (list->requestor_type == NeighList::COMPUTE)
|
||||||
|
&& (compute == list->requestor)
|
||||||
if (list->index == request) {
|
&& (list->id == reqid) ) return i;
|
||||||
return i;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
return -1;
|
return -1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -138,8 +138,8 @@ void *lammps_extract_atom(void *handle, const char *name);
|
|||||||
* Library functions to access data from computes, fixes, variables in LAMMPS
|
* Library functions to access data from computes, fixes, variables in LAMMPS
|
||||||
* ---------------------------------------------------------------------- */
|
* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void *lammps_extract_compute(void *handle, char *id, int, int);
|
void *lammps_extract_compute(void *handle, const char *, int, int);
|
||||||
void *lammps_extract_fix(void *handle, char *, int, int, int, int);
|
void *lammps_extract_fix(void *handle, const char *, int, int, int, int);
|
||||||
void *lammps_extract_variable(void *handle, const char *, const char *);
|
void *lammps_extract_variable(void *handle, const char *, const char *);
|
||||||
int lammps_set_variable(void *, char *, char *);
|
int lammps_set_variable(void *, char *, char *);
|
||||||
|
|
||||||
@ -160,20 +160,20 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data);
|
|||||||
void lammps_scatter_subset(void *handle, char *name, int type, int count, int ndata, int *ids, void *data);
|
void lammps_scatter_subset(void *handle, char *name, int type, int count, int ndata, int *ids, void *data);
|
||||||
|
|
||||||
#if !defined(LAMMPS_BIGBIG)
|
#if !defined(LAMMPS_BIGBIG)
|
||||||
int lammps_create_atoms(void *handle, int n, int *id, int *type,
|
int lammps_create_atoms(void *handle, int n, const int *id, const int *type,
|
||||||
double *x, double *v, int *image, int bexpand);
|
const double *x, const double *v, const int *image, int bexpand);
|
||||||
#else
|
#else
|
||||||
int lammps_create_atoms(void *handle, int n, int64_t *id, int *type,
|
int lammps_create_atoms(void *handle, int n, const int64_t *id, const int *type,
|
||||||
double *x, double *v, int64_t* image, int bexpand);
|
const double *x, const double *v, const int64_t* image, int bexpand);
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
* Library functions for accessing neighbor lists
|
* Library functions for accessing neighbor lists
|
||||||
* ---------------------------------------------------------------------- */
|
* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
int lammps_find_pair_neighlist(void *handle, char *style, int exact, int nsub, int request);
|
int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int nsub, int request);
|
||||||
int lammps_find_fix_neighlist(void *handle, char *id, int request);
|
int lammps_find_fix_neighlist(void *handle, const char *id, int request);
|
||||||
int lammps_find_compute_neighlist(void *handle, char *id, int request);
|
int lammps_find_compute_neighlist(void *handle, const char *id, int request);
|
||||||
int lammps_neighlist_num_elements(void *handle, int idx);
|
int lammps_neighlist_num_elements(void *handle, int idx);
|
||||||
void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, int *numneigh, int **neighbors);
|
void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom, int *numneigh, int **neighbors);
|
||||||
|
|
||||||
|
|||||||
@ -143,6 +143,7 @@ void NeighList::post_constructor(NeighRequest *nq)
|
|||||||
respamiddle = nq->respamiddle;
|
respamiddle = nq->respamiddle;
|
||||||
respainner = nq->respainner;
|
respainner = nq->respainner;
|
||||||
copy = nq->copy;
|
copy = nq->copy;
|
||||||
|
id = nq->id;
|
||||||
|
|
||||||
if (nq->copy) {
|
if (nq->copy) {
|
||||||
listcopy = neighbor->lists[nq->copylist];
|
listcopy = neighbor->lists[nq->copylist];
|
||||||
|
|||||||
@ -44,6 +44,7 @@ class NeighList : protected Pointers {
|
|||||||
int copy; // 1 if this list is copied from another list
|
int copy; // 1 if this list is copied from another list
|
||||||
int kk2cpu; // 1 if this list is copied from Kokkos to CPU
|
int kk2cpu; // 1 if this list is copied from Kokkos to CPU
|
||||||
int copymode; // 1 if this is a Kokkos on-device copy
|
int copymode; // 1 if this is a Kokkos on-device copy
|
||||||
|
int id; // copied from neighbor list request
|
||||||
|
|
||||||
// data structs to store neighbor pairs I,J and associated values
|
// data structs to store neighbor pairs I,J and associated values
|
||||||
|
|
||||||
|
|||||||
@ -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));
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -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;
|
||||||
|
|||||||
@ -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();
|
||||||
};
|
};
|
||||||
|
|||||||
@ -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;
|
||||||
|
|
||||||
|
|||||||
@ -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=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||||
git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
||||||
mkdir hipCUB/build
|
mkdir hipCUB/build
|
||||||
cd hipCUB/build
|
cd hipCUB/build
|
||||||
CXX=hipcc cmake -D BUILD_TEST=off ..
|
CXX=hipcc cmake -D BUILD_TEST=off ..
|
||||||
|
|||||||
@ -2,7 +2,7 @@ BootStrap: docker
|
|||||||
From: ubuntu:20.04
|
From: ubuntu:20.04
|
||||||
|
|
||||||
%environment
|
%environment
|
||||||
export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${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=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||||
git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
||||||
mkdir hipCUB/build
|
mkdir hipCUB/build
|
||||||
cd hipCUB/build
|
cd hipCUB/build
|
||||||
CXX=hipcc cmake -D BUILD_TEST=off ..
|
CXX=hipcc cmake -D BUILD_TEST=off ..
|
||||||
|
|||||||
@ -11,6 +11,7 @@ add_executable(test_library_properties test_library_properties.cpp test_main.cpp
|
|||||||
target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GMock)
|
target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GMock)
|
||||||
target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
|
target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
|
||||||
add_test(LibraryProperties test_library_properties)
|
add_test(LibraryProperties test_library_properties)
|
||||||
|
set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||||
|
|
||||||
set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}")
|
set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}")
|
||||||
set(PKG_COUNT 0)
|
set(PKG_COUNT 0)
|
||||||
|
|||||||
@ -160,7 +160,9 @@ TEST_F(LibraryProperties, box)
|
|||||||
boxlo[0] = -6.1;
|
boxlo[0] = -6.1;
|
||||||
boxhi[1] = 7.3;
|
boxhi[1] = 7.3;
|
||||||
xy = 0.1;
|
xy = 0.1;
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz);
|
lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz);
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
|
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
|
||||||
EXPECT_DOUBLE_EQ(boxlo[0], -6.1);
|
EXPECT_DOUBLE_EQ(boxlo[0], -6.1);
|
||||||
EXPECT_DOUBLE_EQ(boxlo[1], -7.692866);
|
EXPECT_DOUBLE_EQ(boxlo[1], -7.692866);
|
||||||
@ -313,6 +315,121 @@ TEST_F(LibraryProperties, global)
|
|||||||
EXPECT_DOUBLE_EQ((*d_ptr), 0.1);
|
EXPECT_DOUBLE_EQ((*d_ptr), 0.1);
|
||||||
};
|
};
|
||||||
|
|
||||||
|
TEST_F(LibraryProperties, neighlist)
|
||||||
|
{
|
||||||
|
if (!lammps_has_style(lmp, "pair", "sw")) GTEST_SKIP();
|
||||||
|
const char sysinit[] = "boundary f f f\n"
|
||||||
|
"units real\n"
|
||||||
|
"region box block -5 5 -5 5 -5 5\n"
|
||||||
|
"create_box 2 box\n"
|
||||||
|
"mass 1 1.0\n"
|
||||||
|
"mass 2 1.0\n"
|
||||||
|
"pair_style hybrid/overlay lj/cut 4.0 lj/cut 4.0 morse 4.0 sw\n"
|
||||||
|
"pair_coeff * * sw Si.sw Si NULL\n"
|
||||||
|
"pair_coeff 1 2 morse 0.2 2.0 2.0\n"
|
||||||
|
"pair_coeff 2 2 lj/cut 1 0.1 2.0\n"
|
||||||
|
"pair_coeff * * lj/cut 2 0.01 2.0\n"
|
||||||
|
"compute dist all pair/local dist\n"
|
||||||
|
"fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector\n"
|
||||||
|
"thermo_style custom f_dist[*]";
|
||||||
|
|
||||||
|
const double pos[] = {0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
|
||||||
|
0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0};
|
||||||
|
const tagint ids[] = {1, 2, 3, 4, 5, 6, 7};
|
||||||
|
const int types[] = {1, 1, 1, 1, 2, 2, 2};
|
||||||
|
|
||||||
|
const int numatoms = sizeof(ids) / sizeof(tagint);
|
||||||
|
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
|
lammps_commands_string(lmp, sysinit);
|
||||||
|
lammps_create_atoms(lmp, numatoms, ids, types, pos, nullptr, nullptr, 0);
|
||||||
|
lammps_command(lmp, "run 0 post no");
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
|
||||||
|
int nhisto =
|
||||||
|
*(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0);
|
||||||
|
int nskip = *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, 0);
|
||||||
|
double minval =
|
||||||
|
*(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, 0);
|
||||||
|
double maxval =
|
||||||
|
*(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 3, 0);
|
||||||
|
// 21 pair distances counted, none skipped, smallest 1.0, largest 2.1
|
||||||
|
EXPECT_EQ(nhisto, 21);
|
||||||
|
EXPECT_EQ(nskip, 0);
|
||||||
|
EXPECT_DOUBLE_EQ(minval, 1.0);
|
||||||
|
EXPECT_DOUBLE_EQ(maxval, 2.1);
|
||||||
|
|
||||||
|
const int nlocal = lammps_extract_setting(lmp, "nlocal");
|
||||||
|
EXPECT_EQ(nlocal, numatoms);
|
||||||
|
EXPECT_NE(lammps_find_pair_neighlist(lmp, "sw", 1, 0, 0), -1);
|
||||||
|
EXPECT_NE(lammps_find_pair_neighlist(lmp, "morse", 1, 0, 0), -1);
|
||||||
|
EXPECT_NE(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 1, 0), -1);
|
||||||
|
EXPECT_NE(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0), -1);
|
||||||
|
EXPECT_EQ(lammps_find_pair_neighlist(lmp, "lj/cut", 1, 0, 0), -1);
|
||||||
|
EXPECT_EQ(lammps_find_pair_neighlist(lmp, "hybrid/overlay", 1, 0, 0), -1);
|
||||||
|
EXPECT_NE(lammps_find_compute_neighlist(lmp, "dist", 0), -1);
|
||||||
|
EXPECT_EQ(lammps_find_fix_neighlist(lmp, "dist", 0), -1);
|
||||||
|
EXPECT_EQ(lammps_find_compute_neighlist(lmp, "xxx", 0), -1);
|
||||||
|
|
||||||
|
// full neighbor list for 4 type 1 atoms
|
||||||
|
// all have 3 type 1 atom neighbors
|
||||||
|
int idx = lammps_find_pair_neighlist(lmp, "sw", 1, 0, 0);
|
||||||
|
int num = lammps_neighlist_num_elements(lmp, idx);
|
||||||
|
EXPECT_EQ(num, 4);
|
||||||
|
int iatom, inum, *neighbors;
|
||||||
|
for (int i = 0; i < num; ++i) {
|
||||||
|
lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors);
|
||||||
|
EXPECT_EQ(iatom, i);
|
||||||
|
EXPECT_EQ(inum, 3);
|
||||||
|
EXPECT_NE(neighbors, nullptr);
|
||||||
|
}
|
||||||
|
|
||||||
|
// half neighbor list for all pairs between type 1 and type 2
|
||||||
|
// 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors
|
||||||
|
idx = lammps_find_pair_neighlist(lmp, "morse", 0, 0, 0);
|
||||||
|
num = lammps_neighlist_num_elements(lmp, idx);
|
||||||
|
EXPECT_EQ(num, nlocal);
|
||||||
|
for (int i = 0; i < num; ++i) {
|
||||||
|
lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors);
|
||||||
|
if (i < 4)
|
||||||
|
EXPECT_EQ(inum, 3);
|
||||||
|
else
|
||||||
|
EXPECT_EQ(inum, 0);
|
||||||
|
EXPECT_NE(neighbors, nullptr);
|
||||||
|
}
|
||||||
|
|
||||||
|
// half neighbor list between type 2 atoms only
|
||||||
|
// 3 pairs with 2, 1, 0 neighbors
|
||||||
|
idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 1, 0);
|
||||||
|
num = lammps_neighlist_num_elements(lmp, idx);
|
||||||
|
EXPECT_EQ(num, 3);
|
||||||
|
for (int i = 0; i < num; ++i) {
|
||||||
|
lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors);
|
||||||
|
EXPECT_EQ(inum, 2 - i);
|
||||||
|
EXPECT_NE(neighbors, nullptr);
|
||||||
|
}
|
||||||
|
|
||||||
|
// half neighbor list between all pairs. same as simple lj/cut case
|
||||||
|
idx = lammps_find_pair_neighlist(lmp, "lj/cut", 1, 2, 0);
|
||||||
|
num = lammps_neighlist_num_elements(lmp, idx);
|
||||||
|
EXPECT_EQ(num, nlocal);
|
||||||
|
for (int i = 0; i < num; ++i) {
|
||||||
|
lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors);
|
||||||
|
EXPECT_EQ(inum, nlocal - 1 - i);
|
||||||
|
EXPECT_NE(neighbors, nullptr);
|
||||||
|
}
|
||||||
|
|
||||||
|
// the compute has a half neighbor list
|
||||||
|
idx = lammps_find_compute_neighlist(lmp, "dist", 0);
|
||||||
|
num = lammps_neighlist_num_elements(lmp, idx);
|
||||||
|
EXPECT_EQ(num, nlocal);
|
||||||
|
for (int i = 0; i < num; ++i) {
|
||||||
|
lammps_neighlist_element_neighbors(lmp, idx, i, &iatom, &inum, &neighbors);
|
||||||
|
EXPECT_EQ(inum, nlocal - 1 - i);
|
||||||
|
EXPECT_NE(neighbors, nullptr);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
class AtomProperties : public ::testing::Test {
|
class AtomProperties : public ::testing::Test {
|
||||||
protected:
|
protected:
|
||||||
void *lmp;
|
void *lmp;
|
||||||
|
|||||||
@ -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();
|
||||||
|
|||||||
@ -38,7 +38,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -235,41 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// angle_style
|
// angle_style
|
||||||
writer.emit("angle_style", config.angle_style);
|
writer.emit("angle_style", config.angle_style);
|
||||||
@ -340,6 +306,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
TEST(AngleStyle, plain)
|
TEST(AngleStyle, plain)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -566,6 +534,8 @@ TEST(AngleStyle, plain)
|
|||||||
TEST(AngleStyle, omp)
|
TEST(AngleStyle, omp)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
@ -739,6 +709,8 @@ TEST(AngleStyle, omp)
|
|||||||
|
|
||||||
TEST(AngleStyle, single)
|
TEST(AngleStyle, single)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
|
|||||||
@ -38,7 +38,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -235,41 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// bond_style
|
// bond_style
|
||||||
writer.emit("bond_style", config.bond_style);
|
writer.emit("bond_style", config.bond_style);
|
||||||
@ -340,6 +306,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
TEST(BondStyle, plain)
|
TEST(BondStyle, plain)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -566,6 +534,8 @@ TEST(BondStyle, plain)
|
|||||||
TEST(BondStyle, omp)
|
TEST(BondStyle, omp)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
@ -738,6 +708,8 @@ TEST(BondStyle, omp)
|
|||||||
|
|
||||||
TEST(BondStyle, single)
|
TEST(BondStyle, single)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -994,6 +966,8 @@ TEST(BondStyle, single)
|
|||||||
|
|
||||||
TEST(BondStyle, extract)
|
TEST(BondStyle, extract)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
|
|||||||
@ -14,6 +14,7 @@
|
|||||||
#ifndef TEST_CONFIG_H
|
#ifndef TEST_CONFIG_H
|
||||||
#define TEST_CONFIG_H
|
#define TEST_CONFIG_H
|
||||||
|
|
||||||
|
#include <set>
|
||||||
#include <string>
|
#include <string>
|
||||||
#include <utility>
|
#include <utility>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
@ -32,6 +33,7 @@ public:
|
|||||||
std::string date_generated;
|
std::string date_generated;
|
||||||
std::string basename;
|
std::string basename;
|
||||||
double epsilon;
|
double epsilon;
|
||||||
|
std::set<std::string> skip_tests;
|
||||||
std::vector<std::pair<std::string, std::string>> prerequisites;
|
std::vector<std::pair<std::string, std::string>> prerequisites;
|
||||||
std::vector<std::string> pre_commands;
|
std::vector<std::string> pre_commands;
|
||||||
std::vector<std::string> post_commands;
|
std::vector<std::string> post_commands;
|
||||||
@ -74,6 +76,7 @@ public:
|
|||||||
init_vdwl(0), run_vdwl(0), init_coul(0), run_coul(0), init_stress({0, 0, 0, 0, 0, 0}),
|
init_vdwl(0), run_vdwl(0), init_coul(0), run_coul(0), init_stress({0, 0, 0, 0, 0, 0}),
|
||||||
run_stress({0, 0, 0, 0, 0, 0}), global_scalar(0)
|
run_stress({0, 0, 0, 0, 0, 0}), global_scalar(0)
|
||||||
{
|
{
|
||||||
|
skip_tests.clear();
|
||||||
prerequisites.clear();
|
prerequisites.clear();
|
||||||
pre_commands.clear();
|
pre_commands.clear();
|
||||||
post_commands.clear();
|
post_commands.clear();
|
||||||
|
|||||||
@ -15,6 +15,7 @@
|
|||||||
#include "test_config.h"
|
#include "test_config.h"
|
||||||
#include "yaml.h"
|
#include "yaml.h"
|
||||||
#include "yaml_reader.h"
|
#include "yaml_reader.h"
|
||||||
|
#include "utils.h"
|
||||||
|
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
@ -25,11 +26,14 @@
|
|||||||
#include <utility>
|
#include <utility>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
|
|
||||||
|
using LAMMPS_NS::utils::split_words;
|
||||||
|
|
||||||
TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(config)
|
TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(config)
|
||||||
{
|
{
|
||||||
consumers["lammps_version"] = &TestConfigReader::lammps_version;
|
consumers["lammps_version"] = &TestConfigReader::lammps_version;
|
||||||
consumers["date_generated"] = &TestConfigReader::date_generated;
|
consumers["date_generated"] = &TestConfigReader::date_generated;
|
||||||
consumers["epsilon"] = &TestConfigReader::epsilon;
|
consumers["epsilon"] = &TestConfigReader::epsilon;
|
||||||
|
consumers["skip_tests"] = &TestConfigReader::skip_tests;
|
||||||
consumers["prerequisites"] = &TestConfigReader::prerequisites;
|
consumers["prerequisites"] = &TestConfigReader::prerequisites;
|
||||||
consumers["pre_commands"] = &TestConfigReader::pre_commands;
|
consumers["pre_commands"] = &TestConfigReader::pre_commands;
|
||||||
consumers["post_commands"] = &TestConfigReader::post_commands;
|
consumers["post_commands"] = &TestConfigReader::post_commands;
|
||||||
@ -66,6 +70,13 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co
|
|||||||
consumers["equilibrium"] = &TestConfigReader::equilibrium;
|
consumers["equilibrium"] = &TestConfigReader::equilibrium;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
void TestConfigReader::skip_tests(const yaml_event_t &event)
|
||||||
|
{
|
||||||
|
config.skip_tests.clear();
|
||||||
|
for (auto &word : split_words((char *)event.data.scalar.value))
|
||||||
|
config.skip_tests.insert(word);
|
||||||
|
}
|
||||||
|
|
||||||
void TestConfigReader::prerequisites(const yaml_event_t &event)
|
void TestConfigReader::prerequisites(const yaml_event_t &event)
|
||||||
{
|
{
|
||||||
config.prerequisites.clear();
|
config.prerequisites.clear();
|
||||||
|
|||||||
@ -23,6 +23,7 @@ class TestConfigReader : public YamlReader<TestConfigReader> {
|
|||||||
public:
|
public:
|
||||||
TestConfigReader(TestConfig &config);
|
TestConfigReader(TestConfig &config);
|
||||||
|
|
||||||
|
void skip_tests(const yaml_event_t &event);
|
||||||
void prerequisites(const yaml_event_t &event);
|
void prerequisites(const yaml_event_t &event);
|
||||||
void pre_commands(const yaml_event_t &event);
|
void pre_commands(const yaml_event_t &event);
|
||||||
void post_commands(const yaml_event_t &event);
|
void post_commands(const yaml_event_t &event);
|
||||||
|
|||||||
@ -38,7 +38,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -244,41 +243,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// dihedral_style
|
// dihedral_style
|
||||||
writer.emit("dihedral_style", config.dihedral_style);
|
writer.emit("dihedral_style", config.dihedral_style);
|
||||||
@ -343,6 +309,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
TEST(DihedralStyle, plain)
|
TEST(DihedralStyle, plain)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -569,6 +537,8 @@ TEST(DihedralStyle, plain)
|
|||||||
TEST(DihedralStyle, omp)
|
TEST(DihedralStyle, omp)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
|
|||||||
@ -42,7 +42,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -193,41 +192,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
std::string block("");
|
std::string block("");
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// natoms
|
// natoms
|
||||||
writer.emit("natoms", natoms);
|
writer.emit("natoms", natoms);
|
||||||
@ -288,6 +254,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
TEST(FixTimestep, plain)
|
TEST(FixTimestep, plain)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -730,6 +698,8 @@ TEST(FixTimestep, omp)
|
|||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
|
|||||||
@ -38,7 +38,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -235,41 +234,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// improper_style
|
// improper_style
|
||||||
writer.emit("improper_style", config.improper_style);
|
writer.emit("improper_style", config.improper_style);
|
||||||
@ -334,6 +300,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
TEST(ImproperStyle, plain)
|
TEST(ImproperStyle, plain)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -560,6 +528,8 @@ TEST(ImproperStyle, plain)
|
|||||||
TEST(ImproperStyle, omp)
|
TEST(ImproperStyle, omp)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
|
|||||||
@ -16,16 +16,19 @@
|
|||||||
#include "test_config.h"
|
#include "test_config.h"
|
||||||
#include "test_config_reader.h"
|
#include "test_config_reader.h"
|
||||||
#include "utils.h"
|
#include "utils.h"
|
||||||
|
#include "yaml_writer.h"
|
||||||
#include "gmock/gmock.h"
|
#include "gmock/gmock.h"
|
||||||
#include "gtest/gtest.h"
|
#include "gtest/gtest.h"
|
||||||
|
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
#include <ctime>
|
||||||
#include <iostream>
|
#include <iostream>
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
|
|
||||||
using LAMMPS_NS::utils::split_words;
|
using LAMMPS_NS::utils::split_words;
|
||||||
|
using LAMMPS_NS::utils::trim;
|
||||||
|
|
||||||
// common read_yaml_file function
|
// common read_yaml_file function
|
||||||
bool read_yaml_file(const char *infile, TestConfig &config)
|
bool read_yaml_file(const char *infile, TestConfig &config)
|
||||||
@ -37,6 +40,55 @@ bool read_yaml_file(const char *infile, TestConfig &config)
|
|||||||
return true;
|
return true;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// write out common header items for yaml files
|
||||||
|
void write_yaml_header(YamlWriter *writer,
|
||||||
|
TestConfig *cfg,
|
||||||
|
const char *version)
|
||||||
|
{
|
||||||
|
// lammps_version
|
||||||
|
writer->emit("lammps_version", version);
|
||||||
|
|
||||||
|
// date_generated
|
||||||
|
std::time_t now = time(NULL);
|
||||||
|
std::string block = trim(ctime(&now));
|
||||||
|
writer->emit("date_generated", block);
|
||||||
|
|
||||||
|
// epsilon
|
||||||
|
writer->emit("epsilon", cfg->epsilon);
|
||||||
|
|
||||||
|
// skip tests
|
||||||
|
block.clear();
|
||||||
|
for (auto &skip : cfg->skip_tests) {
|
||||||
|
if (block.empty()) block = skip;
|
||||||
|
else block += " " + skip;
|
||||||
|
}
|
||||||
|
writer->emit("skip_tests", block);
|
||||||
|
|
||||||
|
// prerequisites
|
||||||
|
block.clear();
|
||||||
|
for (auto &prerequisite : cfg->prerequisites) {
|
||||||
|
block += prerequisite.first + " " + prerequisite.second + "\n";
|
||||||
|
}
|
||||||
|
writer->emit_block("prerequisites", block);
|
||||||
|
|
||||||
|
// pre_commands
|
||||||
|
block.clear();
|
||||||
|
for (auto &command : cfg->pre_commands) {
|
||||||
|
block += command + "\n";
|
||||||
|
}
|
||||||
|
writer->emit_block("pre_commands", block);
|
||||||
|
|
||||||
|
// post_commands
|
||||||
|
block.clear();
|
||||||
|
for (auto &command : cfg->post_commands) {
|
||||||
|
block += command + "\n";
|
||||||
|
}
|
||||||
|
writer->emit_block("post_commands", block);
|
||||||
|
|
||||||
|
// input_file
|
||||||
|
writer->emit("input_file", cfg->input_file);
|
||||||
|
}
|
||||||
|
|
||||||
// need to be defined in unit test body
|
// need to be defined in unit test body
|
||||||
extern void generate_yaml_file(const char *, const TestConfig &);
|
extern void generate_yaml_file(const char *, const TestConfig &);
|
||||||
|
|
||||||
|
|||||||
@ -22,6 +22,10 @@ extern bool print_stats;
|
|||||||
extern bool verbose;
|
extern bool verbose;
|
||||||
extern std::string INPUT_FOLDER;
|
extern std::string INPUT_FOLDER;
|
||||||
|
|
||||||
|
// convenience method to write out common entries
|
||||||
|
void write_yaml_header(class YamlWriter *writer, TestConfig *cfg,
|
||||||
|
const char *version);
|
||||||
|
|
||||||
#define EXPECT_FP_LE_WITH_EPS(val1, val2, eps) \
|
#define EXPECT_FP_LE_WITH_EPS(val1, val2, eps) \
|
||||||
do { \
|
do { \
|
||||||
const double diff = fabs(val1 - val2); \
|
const double diff = fabs(val1 - val2); \
|
||||||
@ -31,10 +35,11 @@ extern std::string INPUT_FOLDER;
|
|||||||
EXPECT_PRED_FORMAT2(::testing::DoubleLE, err, eps); \
|
EXPECT_PRED_FORMAT2(::testing::DoubleLE, err, eps); \
|
||||||
} while (0);
|
} while (0);
|
||||||
|
|
||||||
#endif
|
|
||||||
|
|
||||||
#if defined _WIN32
|
#if defined _WIN32
|
||||||
static const char PATH_SEP = '\\';
|
static const char PATH_SEP = '\\';
|
||||||
#else
|
#else
|
||||||
static const char PATH_SEP = '/';
|
static const char PATH_SEP = '/';
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
#endif
|
||||||
|
|
||||||
|
|||||||
@ -40,7 +40,6 @@
|
|||||||
#include <cstdio>
|
#include <cstdio>
|
||||||
#include <cstdlib>
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
|
||||||
#include <mpi.h>
|
#include <mpi.h>
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -125,6 +124,13 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new
|
|||||||
command("pair_coeff " + pair_coeff);
|
command("pair_coeff " + pair_coeff);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// set this here explicitly to a setting different
|
||||||
|
// from the default, so we can spot YAML files for
|
||||||
|
// long-range interactions that do not include these
|
||||||
|
// settings. they will fail after restart or read data.
|
||||||
|
command("pair_modify table 0");
|
||||||
|
command("pair_modify table/disp 0");
|
||||||
|
|
||||||
for (auto &post_command : cfg.post_commands) {
|
for (auto &post_command : cfg.post_commands) {
|
||||||
command(post_command);
|
command(post_command);
|
||||||
}
|
}
|
||||||
@ -238,41 +244,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
YamlWriter writer(outfile);
|
YamlWriter writer(outfile);
|
||||||
|
|
||||||
// lammps_version
|
// write yaml header
|
||||||
writer.emit("lammps_version", lmp->version);
|
write_yaml_header(&writer, &test_config, lmp->version);
|
||||||
|
|
||||||
// date_generated
|
|
||||||
std::time_t now = time(NULL);
|
|
||||||
block = ctime(&now);
|
|
||||||
block = block.substr(0, block.find("\n") - 1);
|
|
||||||
writer.emit("date_generated", block);
|
|
||||||
|
|
||||||
// epsilon
|
|
||||||
writer.emit("epsilon", config.epsilon);
|
|
||||||
|
|
||||||
// prerequisites
|
|
||||||
block.clear();
|
|
||||||
for (auto &prerequisite : config.prerequisites) {
|
|
||||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("prerequisites", block);
|
|
||||||
|
|
||||||
// pre_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.pre_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("pre_commands", block);
|
|
||||||
|
|
||||||
// post_commands
|
|
||||||
block.clear();
|
|
||||||
for (auto &command : config.post_commands) {
|
|
||||||
block += command + "\n";
|
|
||||||
}
|
|
||||||
writer.emit_block("post_commands", block);
|
|
||||||
|
|
||||||
// input_file
|
|
||||||
writer.emit("input_file", config.input_file);
|
|
||||||
|
|
||||||
// pair_style
|
// pair_style
|
||||||
writer.emit("pair_style", config.pair_style);
|
writer.emit("pair_style", config.pair_style);
|
||||||
@ -343,6 +316,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
|
|||||||
|
|
||||||
TEST(PairStyle, plain)
|
TEST(PairStyle, plain)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -625,9 +600,14 @@ TEST(PairStyle, plain)
|
|||||||
TEST(PairStyle, omp)
|
TEST(PairStyle, omp)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "omp", "4", "-sf", "omp"};
|
"-pk", "omp", "4", "-sf", "omp"};
|
||||||
|
|
||||||
|
// cannot run dpd styles with more than 1 thread due to using multiple pRNGs
|
||||||
|
if (utils::strmatch(test_config.pair_style, "^dpd")) args[8] = "1";
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
int argc = sizeof(args) / sizeof(char *);
|
int argc = sizeof(args) / sizeof(char *);
|
||||||
|
|
||||||
@ -649,14 +629,6 @@ TEST(PairStyle, omp)
|
|||||||
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
||||||
EXPECT_THAT(output, HasSubstr("Loop time"));
|
EXPECT_THAT(output, HasSubstr("Loop time"));
|
||||||
|
|
||||||
if (utils::strmatch(test_config.pair_style, "^dpd")) {
|
|
||||||
std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n";
|
|
||||||
if (!verbose) ::testing::internal::CaptureStdout();
|
|
||||||
cleanup_lammps(lmp, test_config);
|
|
||||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
|
||||||
GTEST_SKIP();
|
|
||||||
}
|
|
||||||
|
|
||||||
// abort if running in parallel and not all atoms are local
|
// abort if running in parallel and not all atoms are local
|
||||||
const int nlocal = lmp->atom->nlocal;
|
const int nlocal = lmp->atom->nlocal;
|
||||||
ASSERT_EQ(lmp->atom->natoms, nlocal);
|
ASSERT_EQ(lmp->atom->natoms, nlocal);
|
||||||
@ -804,13 +776,136 @@ TEST(PairStyle, omp)
|
|||||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
};
|
};
|
||||||
|
|
||||||
|
TEST(PairStyle, gpu)
|
||||||
|
{
|
||||||
|
if (!LAMMPS::is_installed_pkg("GPU")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
|
const char *args_neigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu"};
|
||||||
|
const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "gpu", "-pk", "gpu", "0", "neigh", "no"};
|
||||||
|
|
||||||
|
char **argv = (char **)args_neigh;
|
||||||
|
int argc = sizeof(args_neigh) / sizeof(char *);
|
||||||
|
|
||||||
|
// cannot use GPU neighbor list with hybrid pair style (yet)
|
||||||
|
if (test_config.pair_style.substr(0, 6) == "hybrid") {
|
||||||
|
argv = (char **)args_noneigh;
|
||||||
|
argc = sizeof(args_noneigh) / sizeof(char *);
|
||||||
|
}
|
||||||
|
|
||||||
|
::testing::internal::CaptureStdout();
|
||||||
|
LAMMPS *lmp = init_lammps(argc, argv, test_config, false);
|
||||||
|
|
||||||
|
std::string output = ::testing::internal::GetCapturedStdout();
|
||||||
|
if (verbose) std::cout << output;
|
||||||
|
|
||||||
|
if (!lmp) {
|
||||||
|
std::cerr << "One or more prerequisite styles with /gpu suffix\n"
|
||||||
|
"are not available in this LAMMPS configuration:\n";
|
||||||
|
for (auto &prerequisite : test_config.prerequisites) {
|
||||||
|
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
|
||||||
|
}
|
||||||
|
GTEST_SKIP();
|
||||||
|
}
|
||||||
|
|
||||||
|
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
||||||
|
EXPECT_THAT(output, HasSubstr("Loop time"));
|
||||||
|
|
||||||
|
// abort if running in parallel and not all atoms are local
|
||||||
|
const int nlocal = lmp->atom->nlocal;
|
||||||
|
ASSERT_EQ(lmp->atom->natoms, nlocal);
|
||||||
|
|
||||||
|
// relax error for GPU package depending on precision setting
|
||||||
|
double epsilon = test_config.epsilon;
|
||||||
|
if (Info::has_accelerator_feature("GPU","precision","double"))
|
||||||
|
epsilon *= 7.5;
|
||||||
|
else if (Info::has_accelerator_feature("GPU","precision","mixed"))
|
||||||
|
epsilon *= 5.0e8;
|
||||||
|
else epsilon *= 1.0e10;
|
||||||
|
// relax test precision when using pppm and single precision FFTs, but only when also running with double precision
|
||||||
|
#if defined(FFT_SINGLE)
|
||||||
|
if (lmp->force->kspace && lmp->force->kspace->compute_flag && Info::has_accelerator_feature("GPU","precision","double"))
|
||||||
|
if (utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
|
||||||
|
#endif
|
||||||
|
const std::vector<coord_t> &f_ref = test_config.init_forces;
|
||||||
|
const std::vector<coord_t> &f_run = test_config.run_forces;
|
||||||
|
ErrorStats stats;
|
||||||
|
|
||||||
|
auto f = lmp->atom->f;
|
||||||
|
auto tag = lmp->atom->tag;
|
||||||
|
stats.reset();
|
||||||
|
for (int i = 0; i < nlocal; ++i) {
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||||
|
}
|
||||||
|
if (print_stats) std::cerr << "init_forces stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
auto pair = lmp->force->pair;
|
||||||
|
auto stress = pair->virial;
|
||||||
|
stats.reset();
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon);
|
||||||
|
if (print_stats) std::cerr << "init_stress stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
stats.reset();
|
||||||
|
EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.init_vdwl, epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.init_coul, epsilon);
|
||||||
|
if (print_stats) std::cerr << "init_energy stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
|
run_lammps(lmp);
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
|
||||||
|
f = lmp->atom->f;
|
||||||
|
tag = lmp->atom->tag;
|
||||||
|
stats.reset();
|
||||||
|
for (int i = 0; i < nlocal; ++i) {
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 5 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 5 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 5 * epsilon);
|
||||||
|
}
|
||||||
|
if (print_stats) std::cerr << "run_forces stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
stress = pair->virial;
|
||||||
|
stats.reset();
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10 * epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10 * epsilon);
|
||||||
|
if (print_stats) std::cerr << "run_stress stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
stats.reset();
|
||||||
|
auto id = lmp->modify->find_compute("sum");
|
||||||
|
auto energy = lmp->modify->compute[id]->compute_scalar();
|
||||||
|
EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon);
|
||||||
|
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon);
|
||||||
|
if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl;
|
||||||
|
|
||||||
|
if (!verbose) ::testing::internal::CaptureStdout();
|
||||||
|
cleanup_lammps(lmp, test_config);
|
||||||
|
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||||
|
};
|
||||||
|
|
||||||
TEST(PairStyle, intel)
|
TEST(PairStyle, intel)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite",
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite",
|
||||||
"-pk", "intel", "0", "mode", "double", "omp",
|
"-pk", "intel", "0", "mode", "double", "omp",
|
||||||
"4", "lrt", "no", "-sf", "intel"};
|
"4", "lrt", "no", "-sf", "intel"};
|
||||||
|
|
||||||
|
// cannot use more than 1 thread for dpd styles due to pRNG
|
||||||
|
if (utils::strmatch(test_config.pair_style, "^dpd")) args[12] = "1";
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
int argc = sizeof(args) / sizeof(char *);
|
int argc = sizeof(args) / sizeof(char *);
|
||||||
|
|
||||||
@ -829,23 +924,6 @@ TEST(PairStyle, intel)
|
|||||||
GTEST_SKIP();
|
GTEST_SKIP();
|
||||||
}
|
}
|
||||||
|
|
||||||
if ((test_config.pair_style == "rebo") || utils::strmatch(test_config.pair_style, "^dpd") ||
|
|
||||||
utils::strmatch(test_config.pair_style, "^tersoff.* shift ")) {
|
|
||||||
std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n";
|
|
||||||
if (!verbose) ::testing::internal::CaptureStdout();
|
|
||||||
cleanup_lammps(lmp, test_config);
|
|
||||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
|
||||||
GTEST_SKIP();
|
|
||||||
}
|
|
||||||
|
|
||||||
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm/disp/intel")) {
|
|
||||||
if (!verbose) ::testing::internal::CaptureStdout();
|
|
||||||
cleanup_lammps(lmp, test_config);
|
|
||||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
|
||||||
std::cerr << "Skipping kspace style pppm/disp/intel\n";
|
|
||||||
GTEST_SKIP();
|
|
||||||
}
|
|
||||||
|
|
||||||
// relax error a bit for USER-INTEL package
|
// relax error a bit for USER-INTEL package
|
||||||
double epsilon = 7.5 * test_config.epsilon;
|
double epsilon = 7.5 * test_config.epsilon;
|
||||||
// relax test precision when using pppm and single precision FFTs
|
// relax test precision when using pppm and single precision FFTs
|
||||||
@ -946,6 +1024,8 @@ TEST(PairStyle, intel)
|
|||||||
TEST(PairStyle, opt)
|
TEST(PairStyle, opt)
|
||||||
{
|
{
|
||||||
if (!LAMMPS::is_installed_pkg("OPT")) GTEST_SKIP();
|
if (!LAMMPS::is_installed_pkg("OPT")) GTEST_SKIP();
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "opt"};
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf", "opt"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -1051,6 +1131,8 @@ TEST(PairStyle, opt)
|
|||||||
|
|
||||||
TEST(PairStyle, single)
|
TEST(PairStyle, single)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
@ -1308,6 +1390,8 @@ TEST(PairStyle, single)
|
|||||||
|
|
||||||
TEST(PairStyle, extract)
|
TEST(PairStyle, extract)
|
||||||
{
|
{
|
||||||
|
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
|
||||||
|
|
||||||
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite"};
|
||||||
|
|
||||||
char **argv = (char **)args;
|
char **argv = (char **)args;
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user