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lammps
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Merge branch 'master' into gpu-unittest 

# Conflicts:
#	unittest/force-styles/test_pair_style.cpp
#	unittest/force-styles/tests/angle-cosine_periodic.yaml
#	unittest/force-styles/tests/mol-pair-born.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_long.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml
#	unittest/force-styles/tests/mol-pair-morse.yaml
#	unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml
This commit is contained in:
Axel Kohlmeyer 2021-04-06 14:45:06 -04:00
parent 232611c184 00e4bdb2b7
commit 190a689354
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
639 changed files with 18575 additions and 11398 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
.github/workflows/unittest-macos.yml vendored
View File

@ -24,7 +24,9 @@ jobs:
shell: bash
working-directory: ${{github.workspace}}/build
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
cmake --build . --parallel 2

21
cmake/CMakeLists.txt
View File

@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools)
set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python)
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)
# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
@ -31,7 +36,7 @@ endif()
# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
if (LAMMPS_INSTALL_RPATH)
if(LAMMPS_INSTALL_RPATH)
set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
endif()
@ -113,7 +118,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
@ -533,6 +538,18 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU
endif()
endforeach()
if(PKG_PLUGIN)
if(BUILD_SHARED_LIBS)
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
else()
message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
endif()
######################################################################
# the windows version of LAMMPS requires a couple extra libraries
# and the MPI library - if use - has to be linked right before those

8
cmake/Modules/Documentation.cmake
View File

@ -55,11 +55,15 @@ if(BUILD_DOC)
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"
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"
EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
EXPECTED_MD5 ${MATHJAX_MD5})
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-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

6
cmake/Modules/GTest.cmake
View File

@ -8,10 +8,12 @@ endif()
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_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
ExternalProject_Add(googletest
URL ${GTEST_URL}
URL_MD5 ecd1fa65e7de707cd5c00bdac56022cd
URL ${GTEST_URL}
URL_MD5 ${GTEST_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

1
cmake/Modules/LAMMPSUtils.cmake
View File

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

17
cmake/Modules/MPI4WIN.cmake
View File

@ -1,16 +1,25 @@
# Download and configure custom MPICH files 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)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
URL_MD5 4939fdb59d13182fd5dd65211e469f14
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
URL_MD5 a61d153500dce44e21b755ee7257e031
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()

10
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,11 +1,13 @@
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)
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
URL ${OPENCL_LOADER_URL}
URL_MD5 011cdcbd41030be94f3fced6d763a52a
URL ${OPENCL_LOADER_URL}
URL_MD5 ${OPENCL_LOADER_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}

23
cmake/Modules/Packages/GPU.cmake
View File

@ -218,7 +218,7 @@ elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED 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()
set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
endif()
@ -226,7 +226,7 @@ elseif(GPU_API STREQUAL "HIP")
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
if(HIP_PLATFORM STREQUAL "hcc")
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED)
@ -284,7 +284,7 @@ elseif(GPU_API STREQUAL "HIP")
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
set(CUBIN_H_FILE "${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)
if(HIP_COMPILER STREQUAL "clang")
@ -338,11 +338,16 @@ elseif(GPU_API STREQUAL "HIP")
if(DOWNLOAD_CUB)
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)
ExternalProject_Add(CUB
GIT_REPOSITORY https://github.com/NVlabs/cub
TIMEOUT 5
URL ${CUB_URL}
URL_MD5 ${CUB_MD5}
PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
@ -354,7 +359,7 @@ elseif(GPU_API STREQUAL "HIP")
else()
find_package(CUB)
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()
@ -381,6 +386,12 @@ elseif(GPU_API STREQUAL "HIP")
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
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()
target_link_libraries(lammps PRIVATE gpu)

8
cmake/Modules/Packages/KIM.cmake
View File

@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
include(ExternalProject)
enable_language(C)
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
URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
URL_MD5 ae1ddda2ef7017ea07934e519d023dca
URL ${KIM_URL}
URL_MD5 ${KIM_MD5}
BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

8
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
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
URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
URL ${KOKKOS_URL}
URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)

8
cmake/Modules/Packages/LATTE.cmake
View File

@ -15,10 +15,14 @@ endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
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)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
URL_MD5 820e73a457ced178c08c71389a385de7
URL ${LATTE_URL}
URL_MD5 ${LATTE_MD5}
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

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

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

7
cmake/Modules/Packages/USER-INTEL.cmake
View File

@ -30,7 +30,12 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
if(Threads_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
target_link_libraries(lammps PRIVATE Threads::Threads)
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

4
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

@ -2,8 +2,4 @@ set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to
set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
target_link_libraries(lammps PRIVATE molfile)

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

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

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

@ -14,15 +14,19 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
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.
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)
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
URL ${SCAFACOS_URL}
URL_MD5 ${SCAFACOS_MD5}
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

8
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -7,10 +7,14 @@ endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
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)
ExternalProject_Add(Eigen3_build
URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
URL_MD5 9e30f67e8531477de4117506fe44669b
URL ${EIGEN3_URL}
URL_MD5 ${EIGEN3_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)

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

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

5
cmake/Modules/YAML.cmake
View File

@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library")
include(ExternalProject)
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_MD5)
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 bb15429d8fb787e7d3f1c83ae129a999
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}

2
cmake/presets/most.cmake
View File

@ -4,7 +4,7 @@
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION

2
doc/src/Build_basics.rst
View File

@ -1,7 +1,7 @@
Basic build options
===================
The following topics are covered on this page, for building both with
The following topics are covered on this page, for building with both
CMake and make:
* :ref:`Serial vs parallel build <serial>`

13
doc/src/Build_extras.rst
View File

@ -125,7 +125,7 @@ CMake build
# default is sm_50
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# 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
# value = yes (default) or no
-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
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.
.. code:: bash
# AMDGPU target
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
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
# CUDA target (not recommended, use GPU_ARCH=cuda)

1
doc/src/Commands_all.rst
View File

@ -86,6 +86,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`plugin <plugin>`
* :doc:`prd <prd>`
* :doc:`print <print>`
* :doc:`processors <processors>`

2
doc/src/Commands_bond.rst
View File

@ -126,7 +126,7 @@ OPT.
* :doc:`quadratic (o) <dihedral_quadratic>`
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
* :doc:`table/cut <dihedral_table>`
.. _improper:

2
doc/src/Commands_pair.rst
View File

@ -187,7 +187,7 @@ OPT.
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mliap <pair_mliap>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`

1
doc/src/Developer.rst
View File

@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community.
Developer_flow
Developer_write
Developer_notes
Developer_plugins
Developer_unittest
Classes
Developer_utils

258
doc/src/Developer_plugins.rst Normal file
View File

@ -0,0 +1,258 @@
Writing plugins
---------------
Plugins provide a mechanism to add functionality to a LAMMPS executable
without recompiling LAMMPS. The functionality for this and the
:doc:`plugin command <plugin>` are implemented in the
:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
Plugins use the operating system's capability to load dynamic shared
object (DSO) files in a way similar shared libraries and then reference
specific functions in those DSOs. Any DSO file with plugins has to include
an initialization function with a specific name, "lammpsplugin_init", that
has to follow specific rules described below. When loading the DSO with
the "plugin" command, this function is looked up and called and will then
register the contained plugin(s) with LAMMPS.
From the programmer perspective this can work because of the object
oriented design of LAMMPS where all pair style commands are derived from
the class Pair, all fix style commands from the class Fix and so on and
usually only functions present in those base classes are called
directly. When a :doc:`pair_style` command or :doc:`fix` command is
issued a new instance of such a derived class is created. This is done
by a so-called factory function which is mapped to the style name. Thus
when, for example, the LAMMPS processes the command ``pair_style lj/cut
2.5``, LAMMPS will look up the factory function for creating the
``PairLJCut`` class and then execute it. The return value of that
function is a ``Pair *`` pointer and the pointer will be assigned to the
location for the currently active pair style.
A DSO file with a plugin thus has to implement such a factory function
and register it with LAMMPS so that it gets added to the map of available
styles of the given category. To register a plugin with LAMMPS an
initialization function has to be present in the DSO file called
``lammpsplugin_init`` which is called with three ``void *`` arguments:
a pointer to the current LAMMPS instance, a pointer to the opened DSO
handle, and a pointer to the registration function. The registration
function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
with information about the plugin and a pointer to the current LAMMPS
instance. Please see below for an example of how the registration is
done.
Members of ``lammpsplugin_t``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
:widths: auto
* - Member
- Description
* - version
- LAMMPS Version string the plugin was compiled for
* - style
- Style of the plugin (pair, bond, fix, command, etc.)
* - name
- Name of the plugin style
* - info
- String with information about the plugin
* - author
- String with the name and email of the author
* - creator.v1
- Pointer to factory function for pair, bond, angle, dihedral, or improper styles
* - creator.v2
- Pointer to factory function for compute, fix, or region styles
* - creator.v3
- Pointer to factory function for command styles
* - handle
- Pointer to the open DSO file handle
Only one of the three alternate creator entries can be used at a time
and which of those is determined by the style of plugin. The "creator.v1"
element is for factory functions of supported styles computing forces (i.e.
pair, bond, angle, dihedral, or improper styles) and the function takes
as single argument the pointer to the LAMMPS instance. The factory function
is cast to the ``lammpsplugin_factory1`` type before assignment. The
"creator.v2" element is for factory functions creating an instance of
a fix, compute, or region style and takes three arguments: a pointer to
the LAMMPS instance, an integer with the length of the argument list and
a ``char **`` pointer to the list of arguments. The factory function pointer
needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
The "creator.v3" element takes the same arguments as "creator.v3" but is
specific to creating command styles: the factory function has to instantiate
the command style locally passing the LAMMPS pointer as argument and then
call its "command" member function with the number and list of arguments.
The factory function pointer needs to be cast to the
``lammpsplugin_factory3`` type before assignment.
Pair style example
^^^^^^^^^^^^^^^^^^
As an example, a hypothetical pair style plugin "morse2" implemented in
a class ``PairMorse2`` in the files ``pair_morse2.h`` and
``pair_morse2.cpp`` with the factory function and initialization
function would look like this:
.. code-block:: C++
#include "lammpsplugin.h"
#include "version.h"
#include "pair_morse2.h"
using namespace LAMMPS_NS;
static Pair *morse2creator(LAMMPS *lmp)
{
return new PairMorse2(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
lammpsplugin_t plugin;
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "morse2";
plugin.info = "Morse2 variant pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
The factory function in this example is called ``morse2creator()``. It
receives a pointer to the LAMMPS class as only argument and thus has to
be assigned to the *creator.v1* member of the plugin struct and cast to the
``lammpsplugin_factory1`` pointer type. It returns a
pointer to the allocated class instance derived from the ``Pair`` class.
This function may be declared static to avoid clashes with other plugins.
The name of the derived class, ``PairMorse2``, must be unique inside
the entire LAMMPS executable.
Fix style example
^^^^^^^^^^^^^^^^^
If the factory function would be for a fix or compute, which take three
arguments (a pointer to the LAMMPS class, the number of arguments and the
list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
Below is an example for that:
.. code-block:: C++
#include "lammpsplugin.h"
#include "version.h"
#include "fix_nve2.h"
using namespace LAMMPS_NS;
static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixNVE2(lmp,argc,argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
lammpsplugin_t plugin;
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "nve2";
plugin.info = "NVE2 variant fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
Command style example
^^^^^^^^^^^^^^^^^^^^^
For command styles there is a third variant of factory function as
demonstrated in the following example, which also shows that the
implementation of the plugin class may also be within the same
file as the plugin interface code:
.. code-block:: C++
#include "lammpsplugin.h"
#include "comm.h"
#include "error.h"
#include "pointers.h"
#include "version.h"
#include <cstring>
namespace LAMMPS_NS {
class Hello : protected Pointers {
public:
Hello(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
};
}
using namespace LAMMPS_NS;
void Hello::command(int argc, char **argv)
{
if (argc != 1) error->all(FLERR,"Illegal hello command");
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
}
static void hellocreator(LAMMPS *lmp, int argc, char **argv)
{
Hello hello(lmp);
hello.command(argc,argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
plugin.version = LAMMPS_VERSION;
plugin.style = "command";
plugin.name = "hello";
plugin.info = "Hello world command v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
Additional Details
^^^^^^^^^^^^^^^^^^
The initialization function **must** be called ``lammpsplugin_init``, it
**must** have C bindings and it takes three void pointers as arguments.
The first is a pointer to the LAMMPS class that calls it and it needs to
be passed to the registration function. The second argument is a
pointer to the internal handle of the DSO file, this needs to be added
to the plugin info struct, so that the DSO can be closed and unloaded
when all its contained plugins are unloaded. The third argument is a
function pointer to the registration function and needs to be stored
in a variable of ``lammpsplugin_regfunc`` type and then called with a
pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
instance as arguments to register a single plugin. There may be multiple
calls to multiple plugins in the same initialization function.
To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
with relevant info: current LAMMPS version string, kind of style, name of
style, info string, author string, pointer to factory function, and the
DSO handle. The registration function is called with a pointer to the address
of this struct and the pointer of the LAMMPS class. The registration function
will then add the factory function of the plugin style to the respective
style map under the provided name. It will also make a copy of the struct
in a list of all loaded plugins and update the reference counter for loaded
plugins from this specific DSO file.
The pair style itself (i.e. the PairMorse2 class in this example) can be
written just like any other pair style that is included in LAMMPS. For
a plugin, the use of the ``PairStyle`` macro in the section encapsulated
by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
name to the style name is done by the plugin registration function with
the information from the ``lammpsplugin_t`` struct. It may be included
in case the new code is intended to be later included in LAMMPS directly.

45
doc/src/Developer_unittest.rst
View File

@ -4,10 +4,10 @@ Adding tests for unit testing
This section discusses adding or expanding tests for the unit test
infrastructure included into the LAMMPS source code distribution.
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
cover as much of the added code as possible. When contributing code to
the distribution, the LAMMPS developers will appreciate if additions
to the integrated unit test facility are included.
of individual features, tend to run fast, and should be set up to cover
as much of the added code as possible. When contributing code to the
distribution, the LAMMPS developers will appreciate if additions to the
integrated unit test facility are included.
Given the complex nature of MD simulations where many operations can
only be performed when suitable "real" simulation environment has been
@ -50,6 +50,9 @@ available:
* - File name:
- Test name:
- Description:
* - ``test_argutils.cpp``
- ArgInfo
- Tests for ``ArgInfo`` class used by LAMMPS
* - ``test_fmtlib.cpp``
- FmtLib
- Tests for ``fmtlib::`` functions used by LAMMPS
@ -155,23 +158,27 @@ have the desired effect:
{
ASSERT_EQ(lmp->update->ntimestep, 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 10");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
END_HIDE_OUTPUT();
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
the LAMMPS command will be silent by capturing the output or not. In
the default case, verbose == false, the test output will be compact and
not mixed with LAMMPS output. However setting the verbose flag (via
setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
helpful to understand why tests fail unexpectedly.
Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
functions that will capture output from running LAMMPS. This is normally
discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
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``
- LatticeRegion
- 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``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`

3
doc/src/Developer_utils.rst
View File

@ -101,6 +101,9 @@ and parsing files or arguments.
.. doxygenfunction:: split_words
:project: progguide
.. doxygenfunction:: split_lines
:project: progguide
.. doxygenfunction:: strmatch
:project: progguide

1
doc/src/Howto_bioFF.rst
View File

@ -91,6 +91,7 @@ documentation for the formula it computes.
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`bond_style <bond_morse>` morse
* :doc:`angle_style <angle_cosine_squared>` cosine/squared
* :doc:`angle_style <angle_harmonic>` harmonic
* :doc:`angle_style <angle_cosine>` cosine
* :doc:`angle_style <angle_cosine_periodic>` cosine/periodic

10
doc/src/Howto_granular.rst
View File

@ -18,12 +18,13 @@ This compute
calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
Use one of these 3 pair potentials, which compute forces and torques
Use one of these 4 pair potentials, which compute forces and torques
between interacting pairs of particles:
* :doc:`pair_style <pair_style>` gran/history
* :doc:`pair_style <pair_style>` gran/no_history
* :doc:`pair_style <pair_style>` gran/hertzian
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/no_history <pair_gran>`
* :doc:`pair_style gran/hertzian <pair_gran>`
* :doc:`pair_style granular <pair_granular>`
These commands implement fix options specific to granular systems:
@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
* :doc:`fix pour <fix_pour>`
* :doc:`fix viscous <fix_viscous>`
* :doc:`fix wall/gran <fix_wall_gran>`
* :doc:`fix wall/gran/region <fix_wall_gran_region>`
The fix style *freeze* zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style

70
doc/src/Install_git.rst
View File

@ -86,33 +86,59 @@ check out any other desired branch) first.
Once you have updated your local files with a ``git pull`` (or ``git
checkout``), you still need to re-build LAMMPS if any source files have
changed. To do this, you should cd to the src directory and type:
changed. How to do this depends on the build system you are using.
.. code-block:: bash
.. tabs::
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
.. tab:: CMake build
just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
Change to your build folder and type:
.. warning::
.. code-block:: bash
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The version in
the source directory is merely a copy and will be wiped out if you type "make
package-update".
cmake . --build
.. warning::
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
The GitHub servers support both the "git://" and
"https://" access protocols for anonymous read-only access. If you
have a correspondingly configured GitHub account, you may also use
SSH access with the URL "git@github.com:lammps/lammps.git".
.. code-block:: bash
The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
Just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".
.. admonition:: Git protocols
:class: note
The servers at github.com support the "git://" and "https://" access
protocols for anonymous, read-only access. If you have a suitably
configured GitHub account, you may also use SSH protocol with the
URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
richard.berger at temple.edu).

62
doc/src/Install_patch.rst
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@ -43,24 +43,54 @@ up to date.
* A list of updated files print out to the screen. The -b switch
creates backup files of your originals (e.g. src/force.cpp.orig), so
you can manually undo the patch if something goes wrong.
* Type the following from the src directory, to enforce consistency
between the src and package directories. This is OK to do even if you
don't use one or more packages. If you are applying several patches
successively, you only need to type this once at the end. The purge
command removes deprecated src files if any were removed by the patch
from package sub-directories.
.. code-block:: bash
* Once you have updated your local files you need to re-build LAMMPS.
If you are applying several patches successively, you only need to
do the rebuild once at the end. How to do it depends on the build
system you are using.
$ make purge
$ make package-update
.. tabs::
* Re-build LAMMPS via the "make" command.
.. tab:: CMake build
.. warning::
Change to your build folder and type:
If you wish to edit/change a source file that is part of a package,
you should edit the version of the file inside the package folder in
src, and then re-install or update the package. The version in the
src directory is merely a copy and will be wiped out when you type
"make package-update".
.. code-block:: bash
cmake . --build
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
.. code-block:: bash
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
to enforce consistency of the source between the src folder
and package directories. This is OK to do even if you don't
use any packages. The "make purge" command removes any deprecated
src files if they were removed by the patch from a package
sub-directory.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".

25
doc/src/Packages_details.rst
View File

@ -50,6 +50,7 @@ page gives those details.
* :ref:`MSCG <PKG-MSCG>`
* :ref:`OPT <PKG-OPT>`
* :ref:`PERI <PKG-PERI>`
* :ref:`PLUGIN <PKG-PLUGIN>`
* :ref:`POEMS <PKG-POEMS>`
* :ref:`PYTHON <PKG-PYTHON>`
* :ref:`QEQ <PKG-QEQ>`
@ -843,6 +844,28 @@ Foster (UTSA).
----------
.. _PKG-PLUGIN:
PLUGIN package
--------------
**Contents:**
A :doc:`plugin <plugin>` command that can load and unload several
kind of styles in LAMMPS from shared object files at runtime without
having to recompile and relink LAMMPS.
**Authors:** Axel Kohlmeyer (Temple U)
**Supporting info:**
* src/PLUGIN: filenames -> commands
* :doc:`plugin command <plugin>`
* :doc:`Information on writing plugins <Developer_plugins>`
* examples/plugin
----------
.. _PKG-POEMS:
POEMS package
@ -2456,6 +2479,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`bond_style mm3 <bond_mm3>`
* :doc:`improper_style distharm <improper_distharm>`
* :doc:`improper_style sqdistharm <improper_sqdistharm>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff

2
doc/src/Packages_standard.rst
View File

@ -71,6 +71,8 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`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:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |

22
doc/src/angle_cosine_periodic.rst
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@ -24,20 +24,17 @@ Examples
Description
"""""""""""
The *cosine/periodic* angle style uses the following potential, which
is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
particularly for organometallic systems where :math:`n` = 4 might be used
The *cosine/periodic* angle style uses the following potential, which may be
particularly used for organometallic systems where :math:`n` = 4 might be used
for an octahedral complex and :math:`n` = 3 might be used for a trigonal
center:
.. math::
E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
@ -47,10 +44,9 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`B` = 1 or -1
* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
Note that the prefactor :math:`C` is specified and not the overall force
constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear
geometry.
Note that the prefactor :math:`C` is specified as coefficient and not the overall force
constant :math:`K = \frac{2 C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry.
----------
@ -75,9 +71,3 @@ Default
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

14
doc/src/angle_cosine_squared.rst
View File

@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential
E = K [\cos(\theta) - \cos(\theta_0)]^2
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
, which is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
is a prefactor. Note that the usual 1/2 factor is included in :math:`K`.
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@ -66,3 +69,10 @@ Default
"""""""
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

1
doc/src/commands_list.rst
View File

@ -77,6 +77,7 @@ Commands
pair_style
pair_write
partition
plugin
prd
print
processors

2
doc/src/dihedral_style.rst
View File

@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
* :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
* :doc:`table <dihedral_table>` - tabulated dihedral
* :doc:`table/cut <dihedral_table_cut>` - tabulated dihedral with analytic cutoff
* :doc:`table/cut <dihedral_table>` - tabulated dihedral with analytic cutoff
----------

89
doc/src/dihedral_table.rst
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@ -1,19 +1,24 @@
.. index:: dihedral_style table
.. index:: dihedral_style table/omp
.. index:: dihedral_style table/cut
dihedral_style table command
============================
Accelerator Variants: *table/omp*
dihedral_style table/cut command
================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style table style Ntable
dihedral_style style interpolation Ntable
* style = *linear* or *spline* = method of interpolation
* style = *table* or *table/cut*
* interpolation = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples
@ -26,13 +31,21 @@ Examples
dihedral_coeff 1 file.table DIH_TABLE1
dihedral_coeff 2 file.table DIH_TABLE2
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
Description
"""""""""""
The *table* dihedral style creates interpolation tables of length
*Ntable* from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". The files are read
by the :doc:`dihedral_coeff <dihedral_coeff>` command.
The *table* and *table/cut* dihedral styles create interpolation tables
of length *Ntable* from dihedral potential and derivative values listed
in a file(s) as a function of the dihedral angle "phi". The files are
read by the :doc:`dihedral_coeff <dihedral_coeff>` command. For
dihedral style *table/cut* additionally an analytic cutoff that is
quadratic in the bond-angle (theta) is applied in order to regularize
the dihedral interaction.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
@ -51,16 +64,53 @@ interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
above.
For dihedral style *table* the following coefficients must be defined
for each dihedral type via the :doc:`dihedral_coeff <dihedral_coeff>`
command as in the example above.
* filename
* keyword
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
The filename specifies a file containing tabulated energy and derivative
values. The keyword specifies which section of the file to read. The
format of this file is the same for both dihedral styles and described
below.
For dihedral style *table/cut* the following coefficients must be
defined for each dihedral type via the :doc:`dihedral_coeff
<dihedral_coeff>` command as in the example above.
* style (aat)
* cutoff prefactor
* cutoff angle1
* cutoff angle2
* filename
* keyword
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
.. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
The cutoff specifies an prefactor to the cutoff function. While this
value would ordinarily equal 1 there may be situations where the value
should change.
The cutoff :math:`\theta_1` specifies the angle (in degrees) below which
the dihedral interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between :math:`\theta_1` and
:math:`\theta_2`, which is the angle at which the cutoff function drops
to zero. The value of zero effectively "turns off" the dihedral
interaction.
The filename specifies a file containing tabulated energy and derivative
values. The keyword specifies which section of the file to read. The
format of this file is the same for both dihedral styles and described
below.
----------
@ -182,18 +232,19 @@ that matches the specified keyword.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This dihedral style writes the settings for the "dihedral_style table"
command to :doc:`binary restart files <restart>`, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
These dihedral styles write the settings for the "dihedral_style table"
or "dihedral_style table/cut" command to :doc:`binary restart files
<restart>`, so a dihedral_style command does not need to specified in an
input script that reads a restart file. However, the coefficient
information loaded from the table file(s) is not stored in the restart
file, since it is tabulated in the potential files. Thus, suitable
dihedral_coeff commands do need to be specified in the restart input
script.
script after reading the restart file.
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
These dihedral styles can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.

229
doc/src/dihedral_table_cut.rst
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@ -1,229 +0,0 @@
.. index:: dihedral_style table/cut
dihedral_style table/cut command
================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style table/cut style Ntable
* style = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples
""""""""
.. code-block:: LAMMPS
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
Description
"""""""""""
The *table/cut* dihedral style creates interpolation tables of length
*Ntable* from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". In addition, an
analytic cutoff that is quadratic in the bond-angle (theta) is applied
in order to regularize the dihedral interaction. The dihedral table
files are read by the :doc:`dihedral_coeff <dihedral_coeff>` command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
*Ntable* dihedral angles. During a simulation, these tables are used
to interpolate energy and force values on individual atoms as
needed. The interpolation is done in one of 2 styles: *linear* or
*spline*\ .
For the *linear* style, the dihedral angle (phi) is used to find 2
surrounding table values from which an energy or its derivative is
computed by linear interpolation.
For the *spline* style, cubic spline coefficients are computed and
stored at each of the *Ntable* evenly-spaced values in the
interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
above.
* style (aat)
* cutoff prefactor
* cutoff angle1
* cutoff angle2
* filename
* keyword
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
.. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
The cutoff specifies an prefactor to the cutoff function. While this value
would ordinarily equal 1 there may be situations where the value should change.
The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral
interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is
the angle at which the cutoff function drops to zero. The value of zero effectively
"turns off" the dihedral interaction.
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
----------
The format of a tabulated file is as follows (without the
parenthesized comments). It can begin with one or more comment
or blank lines.
.. parsed-literal::
# Table of the potential and its negative derivative
DIH_TABLE1 (keyword is the first text on line)
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
(blank line)
1 -168.0 -1.40351172223 0.0423346818422
2 -156.0 -1.70447981034 0.00811786522531
3 -144.0 -1.62956100432 -0.0184129719987
...
30 180.0 -0.707106781187 0.0719306095245
# Example 2: table of the potential. Forces omitted
DIH_TABLE2
N 30 NOF CHECKU testU.dat CHECKF testF.dat
1 -168.0 -1.40351172223
2 -156.0 -1.70447981034
3 -144.0 -1.62956100432
...
30 180.0 -0.707106781187
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
:doc:`dihedral_coeff <dihedral_coeff>` command. The next line lists (in
any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the first value is the index from 1 to N, the second value is
the angle value, the third value is the energy (in energy units), and
the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
are still energy, not force. The dihedral angle values must increase
from one line to the next.
Dihedral table splines are cyclic. There is no discontinuity at 180
degrees (or at any other angle). Although in the examples above, the
angles range from -180 to 180 degrees, in general, the first angle in
the list can have any value (positive, zero, or negative). However
the *range* of angles represented in the table must be *strictly* less
than 360 degrees (2pi radians) to avoid angle overlap. (You may not
supply entries in the table for both 180 and -180, for example.) If
the user's table covers only a narrow range of dihedral angles,
strange numerical behavior can occur in the large remaining gap.
**Parameters:**
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the N
specified in the :doc:`dihedral_style table <dihedral_style>` command.
Let *Ntable* is the number of table entries requested dihedral_style
command, and let *Nfile* be the parameter following "N" in the
tabulated file ("30" in the sparse example above). What LAMMPS does
is a preliminary interpolation by creating splines using the *Nfile*
tabulated values as nodal points. It uses these to interpolate as
needed to generate energy and derivative values at *Ntable* different
points (which are evenly spaced over a 360 degree range, even if the
angles in the file are not). The resulting tables of length *Ntable*
are then used as described above, when computing energy and force for
individual dihedral angles and their atoms. This means that if you
want the interpolation tables of length *Ntable* to match exactly what
is in the tabulated file (with effectively nopreliminary
interpolation), you should set *Ntable* = *Nfile*\ . To insure the
nodal points in the user's file are aligned with the interpolated
table entries, the angles in the table should be integer multiples of
360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the third column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the
interpolated energy table to a file to make sure that the interpolated
function agrees with the user's expectations. (Note: You can
temporarily increase the *Ntable* parameter to a high value for this
purpose. "\ *Ntable*\ " is explained above.)
The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
It is followed by a filename, and it allows the user to check the
interpolated force table. This option is available even if the user
selected the "NOF" option.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This dihedral style writes the settings for the "dihedral_style table/cut"
command to :doc:`binary restart files <restart>`, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
dihedral_coeff commands do need to be specified in the restart input
script.
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`, :doc:`dihedral_style table <dihedral_table>`
Default
"""""""
none
.. _dihedralcut-Salerno:
**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

2
doc/src/dump.rst
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@ -349,7 +349,7 @@ the box size stored with the snapshot.
The *xtc* style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
`here <http://manual.gromacs.org/current/online/xtc.html>`_.
`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
The precision used in XTC files can be adjusted via the
:doc:`dump_modify <dump_modify>` command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC

4
doc/src/fix_ave_chunk.rst
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@ -307,7 +307,9 @@ atoms in the chunk. The averaged output value for the chunk on the
average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep.
the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
kinetic energy are summed separately across the entire *Nfreq* timescale, and
the output value is calculated by dividing those two sums.
If the *norm* setting is *sample*\ , the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"

5
doc/src/fix_cmap.rst
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@ -127,6 +127,11 @@ the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
If you want the potential energy associated with the CMAP terms

12
doc/src/fix_halt.rst
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@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less
overhead in computing bond lengths and not storing them in a separate
compute.
A variable can be used to implement a large variety of conditions,
including to stop when a specific file exists. Example:
.. code-block:: LAMMPS
variable exit equal is_file(EXIT)
fix 10 all halt 100 v_exit != 0 error soft
Will stop the current run command when a file ``EXIT`` is created
in the current working directory. The condition can be cleared
by removing the file through the :doc:`shell <shell>` command.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "\|\^".
In this context, XOR means that if either the attribute or avalue is

4
doc/src/fix_rigid_meso.rst
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@ -48,8 +48,8 @@ Examples
fix 1 ellipsoid rigid/meso single
fix 1 rods rigid/meso molecule
fix 1 spheres rigid/meso single force 1 off off on
fix 1 particles rigid/meso molecule force 1\*5 off off off force 6\*10 off off on
fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque \* off off off
fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off
Description
"""""""""""

8
doc/src/group.rst
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@ -120,12 +120,12 @@ specified atom types, atom IDs, or molecule IDs into the group. These
The first format is a list of values (types or IDs). For example, the
second command in the examples above puts all atoms of type 3 or 4 into
the group named *water*\ . Each entry in the list can be a
colon-separated sequence A:B or A:B:C, as in two of the examples
colon-separated sequence ``A:B`` or ``A:B:C``, as in two of the examples
above. A "sequence" generates a sequence of values (types or IDs),
with an optional increment. The first example with 500:1000 has the
with an optional increment. The first example with ``500:1000`` has the
default increment of 1 and would add all atom IDs from 500 to 1000
(inclusive) to the group sub, along with 10,25,50 since they also
appear in the list of values. The second example with 100:10000:10
appear in the list of values. The second example with ``100:10000:10``
uses an increment of 10 and would thus would add atoms IDs
100,110,120, ... 9990,10000 to the group sub.
@ -269,7 +269,7 @@ group and running further.
.. code-block:: LAMMPS
variable nsteps equal 5000
variable rad equal 18-(step/v_nsteps)\*(18-5)
variable rad equal 18-(step/v_nsteps)*(18-5)
region ss sphere 20 20 0 v_rad
group mobile dynamic all region ss
fix 1 mobile nve

2
doc/src/kim_commands.rst
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@ -1205,7 +1205,7 @@ coordinates of atoms in the unit cell of the cubic crystal. In the case of,
e.g. a conventional fcc unit cell, the "source-value" key in the map associated
with this key should be assigned the following value:
.. code-block:: LAMMPS
.. code-block:: text
[[0.0, 0.0, 0.0],
[0.5, 0.5, 0.0],

2
doc/src/pair_dpd.rst
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@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc.
The :doc:`pair_modify <pair_modify>` table option is not relevant
for these pair styles.
These pair style do not support the :doc:`pair_modify <pair_modify>`
These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.

2
doc/src/pair_fep_soft.rst
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@ -363,7 +363,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info
The different versions of the *lj/cut/soft* pair styles support mixing. For
atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma`
coefficients and cutoff distance for these pair style can be mixed. The default
coefficients and cutoff distance for these pair styles can be mixed. The default
mix value is *geometric* for 12-6 styles.
The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to

2
doc/src/pair_gayberne.rst
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@ -188,7 +188,7 @@ Restrictions
The *gayberne* style is part of the ASPHERE package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These pair style require that atoms store torque and a quaternion to
These pair styles require that atoms store torque and a quaternion to
represent their orientation, as defined by the
:doc:`atom_style <atom_style>`. It also require they store a per-type
:doc:`shape <set>`. The particles cannot store a per-particle

55
doc/src/pair_lj_switch3_coulgauss_long.rst
View File

@ -1,8 +1,12 @@
.. index:: pair_style lj/switch3/coulgauss/long
.. index:: pair_style mm3/switch3/coulgauss/long
pair_style lj/switch3/coulgauss/long command
============================================
pair_style mm3/switch3/coulgauss/long command
=============================================
Syntax
""""""
@ -10,7 +14,7 @@ Syntax
pair_style style args
* style = *lj/switch3/coulgauss/long*
* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long*
* args = list of arguments for a particular style
.. parsed-literal::
@ -20,6 +24,11 @@ Syntax
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
Examples
""""""""
@ -31,6 +40,12 @@ Examples
pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
Description
"""""""""""
@ -41,8 +56,17 @@ vdW potential
E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
, which goes smoothly to zero at the cutoff r_c as defined
by the switching function
The *mm3/switch3/coulgauss/long* style evaluates the MM3
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
Both potentials go smoothly to zero at the cutoff r_c as defined by the
switching function
.. math::
@ -85,14 +109,35 @@ commands:
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/long pair styles can be mixed.
The default mix value is *geometric*\ . See the "pair_modify" command
for details.
Shifting the potential energy is not necessary because the switching
function ensures that the potential is zero at the cut-off.
These pair styles support the :doc:`pair_modify <pair_modify>` table and
options since they can tabulate the short-range portion of the
long-range Coulombic interactions.
Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.
These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*\ , *middle*\ , *outer* keywords.
Restrictions
""""""""""""
These styles are part of the USER-YAFF package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These styles are part of the USER-YAFF package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""

109
doc/src/pair_mm3_switch3_coulgauss_long.rst
View File

@ -1,109 +0,0 @@
.. index:: pair_style mm3/switch3/coulgauss/long
pair_style mm3/switch3/coulgauss/long command
=============================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = *mm3/switch3/coulgauss/long*
* args = list of arguments for a particular style
.. parsed-literal::
*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style mm3/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
Description
"""""""""""
The *mm3/switch3/coulgauss/long* style evaluates the MM3
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
, which goes smoothly to zero at the cutoff r_c as defined
by the switching function
.. math::
S_3(r) = \left\lbrace \begin{array}{ll}
1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
\end{array} \right.
where w is the width defined in the arguments. This potential
is combined with Coulomb interaction between Gaussian charge densities:
.. math::
E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,
epsilon is the dielectric constant which can be set by the
:doc:`dielectric <dielectric>` command, ::math:`\gamma_i` and
:math:`\gamma_j` are the widths of the Gaussian charge distribution and
erf() is the error-function. This style has to be used in conjunction
with the :doc:`kspace_style <kspace_style>` command
If one cutoff is specified it is used for both the vdW and Coulomb
terms. If two cutoffs are specified, the first is used as the cutoff
for the vdW terms, and the second is the cutoff for the Coulombic term.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`\epsilon` (energy)
* :math:`r_v` (distance)
* :math:`\gamma` (distance)
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Mixing rules are fixed for this style as defined above.
Shifting the potential energy is not necessary because the switching
function ensures that the potential is zero at the cut-off.
Restrictions
""""""""""""
These styles are part of the USER-YAFF package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none

2
doc/src/pair_polymorphic.rst
View File

@ -319,7 +319,7 @@ This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This pair potential requires the :doc:`newtion <newton>` setting to be
This pair potential requires the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The potential files provided with LAMMPS (see the potentials directory)

2
doc/src/pair_style.rst
View File

@ -250,7 +250,7 @@ accelerated styles exist.
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
* :doc:`mie/cut <pair_mie>` - Mie potential
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
* :doc:`morse <pair_morse>` - Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential

2
doc/src/pair_vashishta.rst
View File

@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
These pair style are part of the MANYBODY package. They is only
These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These pair styles requires the :doc:`newton <newton>` setting to be "on"

90
doc/src/plugin.rst Normal file
View File

@ -0,0 +1,90 @@
.. index:: plugin
plugin command
==============
Syntax
""""""
.. parsed-literal::
plugin command args
* command = *load* or *unload* or *list* or *clear*
* args = list of arguments for a particular plugin command
.. parsed-literal::
*load* file = load plugin(s) from shared object in *file*
*unload* style name = unload plugin *name* of style *style*
*style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *compute* or *fix* or *region* or *command*
*list* = print a list of currently loaded plugins
*clear* = unload all currently loaded plugins
Examples
""""""""
.. code-block:: LAMMPS
plugin load morse2plugin.so
plugin unload pair morse2/omp
plugin unload command hello
plugin list
plugin clear
Description
"""""""""""
The plugin command allows to load (and unload) additional styles and
commands into a LAMMPS binary from so-called dynamic shared object (DSO)
files. This enables to add new functionality to an existing LAMMPS
binary without having to recompile and link the entire executable.
The *load* command will load and initialize all plugins contained in the
plugin DSO with the given filename. A message with information the
plugin style and name and more will be printed. Individual DSO files
may contain multiple plugins. More details about how to write and
compile the plugin DSO is given in programmer's guide part of the manual
under :doc:`Developer_plugins`.
The *unload* command will remove the given style or the given name from
the list of available styles. If the plugin style is currently in use,
that style instance will be deleted.
The *list* command will print a list of the loaded plugins and their
styles and names.
The *clear* command will unload all currently loaded plugins.
Restrictions
""""""""""""
The *plugin* command is part of the PLUGIN package. It is
only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for
more info. Plugins are not available on Windows.
For the loading of plugins to work the LAMMPS library must be
:ref:`compiled as a shared library <library>`. If plugins
access functions or classes from a package, LAMMPS must have
been compiled with that package included.
Plugins are dependent on the LAMMPS binary interface (ABI)
and particularly the MPI library used. So they are not guaranteed
to work when the plugin was compiled with a different MPI library
or different compilation settings or a different LAMMPS version.
There are no checks, so if there is a mismatch the plugin object
will either not load or data corruption and crashes may happen.
Related commands
""""""""""""""""
none
Default
"""""""
none

9
doc/src/rerun.rst
View File

@ -15,7 +15,7 @@ Syntax
.. 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
Nfirst = dump timestep to start on
*last* args = Nlast
@ -28,6 +28,7 @@ Syntax
Nstart = timestep on which pseudo run will start
*stop* args = Nstop
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
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
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.
Its arguments are passed internally to the :doc:`read_dump <read_dump>`
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
infinity), start = same as first, stop = same as last, every = 0, skip
= 1;
= 1, post = no;

2
doc/src/units.rst
View File

@ -87,7 +87,7 @@ energy is a derived unit (in SI units you equivalently have the relation
* charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}`
* dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}`
* electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}`
* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}`
* density = mass/volume, where :math:`\rho^* = \rho \frac{\sigma^{dim}}{m}`
Note that for LJ units, the default mode of thermodynamic output via
the :doc:`thermo_style <thermo_style>` command is to normalize all

10
doc/src/variable.rst
View File

@ -65,8 +65,8 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name)
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
@ -429,7 +429,7 @@ argument. For *equal*\ -style variables the formula computes a scalar
quantity, which becomes the value of the variable whenever it is
evaluated. For *vector*\ -style variables the formula must compute a
vector of quantities, which becomes the value of the variable whenever
it is evaluated. The calculated vector can be on length one, but it
it is evaluated. The calculated vector can be of length one, but it
cannot be a simple scalar value like that produced by an equal-style
compute. I.e. the formula for a vector-style variable must have at
least one quantity in it that refers to a global vector produced by a
@ -821,6 +821,10 @@ Special Functions
Special functions take specific kinds of arguments, meaning their
arguments cannot be formulas themselves.
The is_file(x) function is a test whether 'x' is a (readable) file
and returns 1 in this case, otherwise it returns 0. For that 'x'
is taken as a literal string and must not have any blanks in it.
The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
"f_ID" or "f_ID[N]" or "v_name". The first two are computes and the

6
doc/utils/sphinx-config/LAMMPSLexer.py
View File

@ -40,7 +40,7 @@ class LAMMPSLexer(RegexLexer):
(r'compute\s+', Keyword, 'compute'),
(r'dump\s+', Keyword, 'dump'),
(r'region\s+', Keyword, 'region'),
(r'variable\s+', Keyword, 'variable'),
(r'^\s*variable\s+', Keyword, 'variable_cmd'),
(r'group\s+', Keyword, 'group'),
(r'change_box\s+', Keyword, 'change_box'),
(r'uncompute\s+', Keyword, 'uncompute'),
@ -51,6 +51,7 @@ class LAMMPSLexer(RegexLexer):
(r'#.*?\n', Comment),
('"', String, 'string'),
('\'', String, 'single_quote_string'),
(r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
(r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
('\$?\(', Name.Variable, 'expression'),
('\$\{', Name.Variable, 'variable'),
@ -58,6 +59,7 @@ class LAMMPSLexer(RegexLexer):
(r'\$[\w_]+', Name.Variable),
(r'\s+', Whitespace),
(r'[\+\-\*\^\|\/\!%&=<>]', Operator),
(r'[\~\.\w_:,@\-\/\\0-9]+', Text),
],
'keywords' : [
(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
@ -99,7 +101,7 @@ class LAMMPSLexer(RegexLexer):
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],
'variable' : [
'variable_cmd' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -1588,6 +1588,7 @@ lammps
Lammps
LAMMPS
lammpsplot
lammpsplugin
Lampis
Lamoureux
Lanczos

56
examples/deposit/in.deposit.molecule.rigid-small Normal file
View 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/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

4
examples/deposit/in.deposit.molecule.shake
View File

@ -21,11 +21,11 @@ bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
group addatoms empty
region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms nve

218
examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 Normal file
View File

@ -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/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 1.0958952 -6.6412275 -6.5813425 -0.68789614
900 368 1.1250033 -6.6101882 -6.541404 -0.66674346
1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868
1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356
1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362
1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732
1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126
1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725
1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781
1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614
1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325
1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549
2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916
2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192
2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829
2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081
2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327
2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961
2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215
2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942
2800 406 0.48039778 -6.5715192 -6.488692 -0.753758
2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541
3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351
3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518
3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546
3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083
3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877
3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211
3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102
3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914
3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328
3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515
4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096
4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103
4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697
4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035
4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855
4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115
4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212
4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052
4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313
4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121
5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083
5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209
5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689
5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364
5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784
5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279
5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812
5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129
5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487
5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808
6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449
6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022
6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158
6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756
6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022
6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635
6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269
6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486
6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583
6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423
7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516
7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333
7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478
7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023
7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428
7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988
7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613
7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595
7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222
7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992
8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866
8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659
8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713
8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592
8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264
8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317
8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203
8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986
8800 526 0.28868972 -6.7159628 -6.595218 -0.876093
8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125
9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897
9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143
9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096
9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522
9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612
9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439
9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372
9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151
9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769
9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604
10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882
Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms
Performance: 249924.414 tau/day, 578.529 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.637 | 9.637 | 9.637 | 0.0 | 55.75
Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15
Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11
Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79
Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06
Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67
Other | | 0.08248 | | | 0.48
Nlocal: 550.000 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2367.00 ave 2367 max 2367 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 36781.0 ave 36781 max 36781 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36781
Ave neighs/atom = 66.874545
Ave special neighs/atom = 0.36363636
Neighbor list builds = 840
Dangerous builds = 0
Total wall time: 0:00:17

218
examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 Normal file
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@ -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 = 0.139 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/small molecule mol dimer
create bodies CPU = 0.006 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 1.0958893 -6.6402029 -6.5803182 -0.66307281
900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928
1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019
1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939
1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897
1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289
1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931
1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968
1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869
1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465
1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236
1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463
2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888
2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981
2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822
2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417
2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938
2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179
2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067
2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914
2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562
2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427
3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127
3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445
3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608
3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883
3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204
3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901
3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264
3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431
3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667
3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122
4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967
4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037
4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753
4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696
4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548
4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593
4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746
4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162
4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822
4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531
5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472
5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418
5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959
5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927
5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219
5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653
5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644
5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043
5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597
5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958
6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837
6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744
6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451
6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495
6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003
6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805
6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134
6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239
6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552
6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238
7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162
7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435
7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949
7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835
7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158
7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236
7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904
7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369
7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511
7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214
8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054
8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067
8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587
8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704
8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503
8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489
8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456
8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994
8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619
8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898
9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499
9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309
9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755
9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234
9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501
9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525
9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541
9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149
9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064
9900 548 0.31832347 -6.790661 -6.6468926 -1.006
10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518
Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms
Performance: 124259.065 tau/day, 287.637 timesteps/s
73.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00
Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03
Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59
Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21
Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29
Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57
Other | | 1.499 | | | 4.31
Nlocal: 137.500 ave 299 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1898.75 ave 2679 max 524 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9204.00 ave 23014 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36816
Ave neighs/atom = 66.938182
Ave special neighs/atom = 0.36363636
Neighbor list builds = 832
Dangerous builds = 0
Total wall time: 0:00:34

48
examples/gcmc/in.gcmc.co2
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@ -1,4 +1,4 @@
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# GCMC for CO2 molecular fluid, rigid/small dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
@ -7,7 +7,7 @@
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
@ -17,7 +17,7 @@ variable spacing index 5.0
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
@ -25,7 +25,7 @@ angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc ${spacing}
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
create_box 2 box &
bond/types 1 &
@ -34,56 +34,56 @@ create_box 2 box &
extra/angle/per/atom 1 &
extra/special/per/atom 2
molecule co2mol CO2.txt
create_atoms 0 box mol co2mol 464563 units box
# rigid CO2 TraPPE model
create_atoms 0 box mol co2mol 464563 units box
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create ${temp} 54654
timestep 1.0
# rigid constraints with thermostat
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigid co2 rigid/small molecule mol co2mol
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
fix_modify myrigid dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
co2mol tfac_insert ${tfac} group co2 rigid myrigid
# atom counts
variable carbon atom "type==1"
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes

196
examples/gcmc/log.27Nov18.gcmc.co2.g++.1
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@ -1,196 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00134993 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, 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) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10
2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12
3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24
4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24
5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18
6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12
7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4
8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16
9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14
10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16
11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20
12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28
13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10
14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10
15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22
16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2
17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18
18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6
19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10
20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18
Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms
Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63
Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11
Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80
Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54
Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28
Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01
Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45
Other | | 0.03692 | | | 0.18
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2081 ave 2081 max 2081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6264 ave 6264 max 6264 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6264
Ave neighs/atom = 232
Ave special neighs/atom = 2
Neighbor list builds = 20177
Dangerous builds = 0
Total wall time: 0:00:21

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LAMMPS (10 Mar 2021)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule template co2mol:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
create_atoms CPU = 0.002 seconds
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigid co2 rigid/small molecule mol co2mol
create bodies CPU = 0.000 seconds
8 rigid bodies with 24 atoms
1.1600000 = max distance from body owner to body atom
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigid dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.16463644
estimated absolute RMS force accuracy = 0.033206372
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, 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) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14
2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10
3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12
4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18
5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20
6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20
7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10
8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10
9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6
10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24
11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16
12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22
13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20
14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18
15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20
16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8
17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4
18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12
19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16
20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6
Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms
Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94
Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17
Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02
Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59
Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15
Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00
Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84
Other | | 0.05594 | | | 0.29
Nlocal: 9.00000 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 703.000 ave 703 max 703 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 719.000 ave 719 max 719 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 719
Ave neighs/atom = 79.888889
Ave special neighs/atom = 2.0000000
Neighbor list builds = 20196
Dangerous builds = 0
Total wall time: 0:00:19

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/build*

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##########################################
# CMake build system for plugin examples.
# The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package.
##########################################
cmake_minimum_required(VERSION 3.10)
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
project(plugins VERSION 1.0 LANGUAGES CXX)
# NOTE: the next line should be commented out when used outside of the LAMMPS package
get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE)
set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers")
if(NOT LAMMPS_HEADER_DIR)
message(FATAL_ERROR "Must set LAMMPS_HEADER_DIR")
endif()
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# bail out on windows
if(CMAKE_SYSTEM_NAME STREQUAL Windows)
message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows")
endif()
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfaceCXX)
##########################
# building the plugins
add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp)
target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP")
target_link_libraries(morse2plugin PRIVATE lammps)
add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp)
target_link_libraries(nve2plugin PRIVATE lammps)
add_library(helloplugin MODULE helloplugin.cpp)
target_link_libraries(helloplugin PRIVATE lammps)
add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp
angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp)
target_link_libraries(zero2plugin PRIVATE lammps)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
PREFIX ""
LINK_FLAGS "-rdynamic")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
endif()

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# Cmake script code to define the LAMMPS C++ interface
# settings required for building LAMMPS plugins
################################################################################
# helper function
function(validate_option name values)
string(TOLOWER ${${name}} needle_lower)
string(TOUPPER ${${name}} needle_upper)
list(FIND ${values} ${needle_lower} IDX_LOWER)
list(FIND ${values} ${needle_upper} IDX_UPPER)
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
message(FATAL_ERROR "\n########################################################################\n"
"Invalid value '${${name}}' for option ${name}\n"
"\n"
"Possible values are:\n"
"${POSSIBLE_VALUE_LIST}"
"########################################################################")
endif()
endfunction(validate_option)
#################################################################################
# LAMMPS C++ interface. We only need the header related parts.
add_library(lammps INTERFACE)
target_include_directories(lammps INTERFACE ${LAMMPS_HEADER_DIR})
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
endif()
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
else()
target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
endif()
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
################################################################################
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
else()
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
endif()
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
endif()

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CXX=mpicxx
CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp
LD=$(CXX) -shared -rdynamic -fopenmp
DSOEXT=.so
include Makefile.common

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default: morse2plugin$(DSOEXT) nve2plugin$(DSOEXT) helloplugin$(DSOEXT) zero2plugin$(DSOEXT)
helloplugin$(DSOEXT): helloplugin.o
$(LD) -o $@ $^
morse2plugin$(DSOEXT): morse2plugin.o pair_morse2.o pair_morse2_omp.o
$(LD) -o $@ $^
nve2plugin$(DSOEXT): nve2plugin.o fix_nve2.o
$(LD) -o $@ $^
zero2plugin$(DSOEXT): zero2plugin.o pair_zero2.o bond_zero2.o angle_zero2.o dihedral_zero2.o improper_zero2.o
$(LD) -o $@ $^
.cpp.o:
$(CXX) -o $@ $(CXXFLAGS) -c $<
helloplugin.o: helloplugin.cpp
pair_morse2.o: pair_morse2.cpp pair_morse2.h
pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h
morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h
fix_nve2.o: fix_nve2.cpp fix_nve2.h
nve2plugin.o: nve2plugin.cpp fix_nve2.h
pair_zero2.o: pair_zero2.cpp pair_zero2.h
bond_zero2.o: bond_zero2.cpp bond_zero2.h
angle_zero2.o: angle_zero2.cpp angle_zero2.h
dihedral_zero2.o: dihedral_zero2.cpp dihedral_zero2.h
improper_zero2.o: improper_zero2.cpp improper_zero2.h
zero2plugin.o: zero2plugin.cpp pair_zero2.h bond_zero2.h angle_zero2.h dihedral_zero2.h
clean:
rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles

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CXX=mpicxx
CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP
LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup
DSOEXT=.dylib
include Makefile.common

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CXX=g++
CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp
LD=$(CXX) -shared -rdynamic -fopenmp
DSOEXT=.so
include Makefile.common

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
#include "angle_zero2.h"
#include "atom.h"
#include "comm.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
AngleZero2::AngleZero2(LAMMPS *lmp) : Angle(lmp), coeffflag(1) {}
/* ---------------------------------------------------------------------- */
AngleZero2::~AngleZero2()
{
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(theta0);
}
}
/* ---------------------------------------------------------------------- */
void AngleZero2::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void AngleZero2::settings(int narg, char **arg)
{
if ((narg != 0) && (narg != 1))
error->all(FLERR,"Illegal angle_style command");
if (narg == 1) {
if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
else error->all(FLERR,"Illegal angle_style command");
}
}
/* ---------------------------------------------------------------------- */
void AngleZero2::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(theta0,n+1,"angle:theta0");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleZero2::coeff(int narg, char **arg)
{
if ((narg < 1) || (coeffflag && narg > 2))
error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
double theta0_one = 0.0;
if (coeffflag && (narg == 2))
theta0_one = utils::numeric(FLERR,arg[1],false,lmp);
// convert theta0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
setflag[i] = 1;
theta0[i] = theta0_one/180.0 * MY_PI;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleZero2::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleZero2::write_restart(FILE *fp) {
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleZero2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
}
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void AngleZero2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g\n",i,theta0[i]/MY_PI*180.0);
}
/* ---------------------------------------------------------------------- */
double AngleZero2::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/)
{
return 0.0;
}

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/* -*- 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_ANGLE_ZERO2_H
#define LMP_ANGLE_ZERO2_H
#include "angle.h"
namespace LAMMPS_NS {
class AngleZero2 : public Angle {
public:
AngleZero2(class LAMMPS *);
virtual ~AngleZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
double single(int, int, int, int);
protected:
double *theta0;
int coeffflag;
void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for angle coefficients
Self-explanatory. Check the input script or data file.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
#include "bond_zero2.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "memory.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondZero2::BondZero2(LAMMPS *lmp) : Bond(lmp), coeffflag(1) {}
/* ---------------------------------------------------------------------- */
BondZero2::~BondZero2()
{
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(r0);
}
}
/* ---------------------------------------------------------------------- */
void BondZero2::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void BondZero2::settings(int narg, char **arg)
{
if ((narg != 0) && (narg != 1))
error->all(FLERR,"Illegal bond_style command");
if (narg == 1) {
if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
else error->all(FLERR,"Illegal bond_style command");
}
}
/* ---------------------------------------------------------------------- */
void BondZero2::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(r0,n+1,"bond:r0");
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void BondZero2::coeff(int narg, char **arg)
{
if ((narg < 1) || (coeffflag && narg > 2))
error->all(FLERR,"Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
double r0_one = 0.0;
if (coeffflag && (narg == 2))
r0_one = utils::numeric(FLERR,arg[1],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
setflag[i] = 1;
r0[i] = r0_one;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondZero2::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondZero2::write_restart(FILE *fp) {
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondZero2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
}
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void BondZero2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++)
fprintf(fp,"%d %g\n",i,r0[i]);
}
/* ---------------------------------------------------------------------- */
double BondZero2::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/,
double & /*fforce*/)
{
return 0.0;
}
/* ---------------------------------------------------------------------- */
void *BondZero2::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str,"r0")==0) return (void*) r0;
return nullptr;
}

58
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/* -*- 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_BOND_ZERO2_H
#define LMP_BOND_ZERO2_H
#include "bond.h"
namespace LAMMPS_NS {
class BondZero2 : public Bond {
public:
BondZero2(class LAMMPS *);
virtual ~BondZero2();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
double single(int, double, int, int, double &);
virtual void *extract(const char *, int &);
protected:
double *r0;
int coeffflag;
virtual void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for bond coefficients
Self-explanatory. Check the input script or data file.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
#include "dihedral_zero2.h"
#include "atom.h"
#include "error.h"
#include "memory.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DihedralZero2::DihedralZero2(LAMMPS *lmp) : Dihedral(lmp), coeffflag(1)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
DihedralZero2::~DihedralZero2()
{
if (allocated && !copymode) {
memory->destroy(setflag);
}
}
/* ---------------------------------------------------------------------- */
void DihedralZero2::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void DihedralZero2::settings(int narg, char **arg)
{
if ((narg != 0) && (narg != 1))
error->all(FLERR,"Illegal dihedral_style command");
if (narg == 1) {
if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
else error->all(FLERR,"Illegal dihedral_style command");
}
}
/* ---------------------------------------------------------------------- */
void DihedralZero2::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void DihedralZero2::coeff(int narg, char **arg)
{
if ((narg < 1) || (coeffflag && narg > 1))
error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralZero2::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralZero2::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralZero2::write_data(FILE *fp) {
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d\n",i);
}

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/* -*- 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.
Identical to dihedral harmonic, except if all k's are zero the
force loop is skipped.
------------------------------------------------------------------------- */
#ifndef LMP_DIHEDRAL_ZERO2_H
#define LMP_DIHEDRAL_ZERO2_H
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralZero2 : public Dihedral {
public:
DihedralZero2(class LAMMPS *);
virtual ~DihedralZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
int coeffflag;
virtual void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for dihedral coefficients
UNDOCUMENTED
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
#include "fix_nve2.h"
#include <cstring>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNVE2::FixNVE2(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (strcmp(style,"nve/sphere") != 0 && narg < 3)
error->all(FLERR,"Illegal fix nve command");
dynamic_group_allow = 1;
time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixNVE2::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNVE2::init()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa"))
step_respa = ((Respa *) update->integrate)->step;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixNVE2::initial_integrate(int /*vflag*/)
{
double dtfm;
// update v and x of atoms in group
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVE2::final_integrate()
{
double dtfm;
// update v of atoms in group
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVE2::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
// innermost level - NVE update of v and x
// all other levels - NVE update of v
if (ilevel == 0) initial_integrate(vflag);
else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVE2::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVE2::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}

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/* -*- 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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(nve2,FixNVE2)
#else
#ifndef LMP_FIX_NVE2_H
#define LMP_FIX_NVE2_H
#include "fix.h"
namespace LAMMPS_NS {
class FixNVE2 : public Fix {
public:
FixNVE2(class LAMMPS *, int, char **);
virtual ~FixNVE2() {}
int setmask();
virtual void init();
virtual void initial_integrate(int);
virtual void final_integrate();
virtual void initial_integrate_respa(int, int, int);
virtual void final_integrate_respa(int, int);
virtual void reset_dt();
protected:
double dtv,dtf;
double *step_respa;
int mass_require;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/

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#include "lammpsplugin.h"
#include "comm.h"
#include "error.h"
#include "pointers.h"
#include "version.h"
#include <cstring>
namespace LAMMPS_NS {
class Hello : protected Pointers {
public:
Hello(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
};
}
using namespace LAMMPS_NS;
void Hello::command(int argc, char **argv)
{
if (argc != 1) error->all(FLERR,"Illegal hello command");
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
}
static void hellocreator(LAMMPS *lmp, int argc, char **argv)
{
Hello hello(lmp);
hello.command(argc,argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
plugin.version = LAMMPS_VERSION;
plugin.style = "command";
plugin.name = "hello";
plugin.info = "Hello world command v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
#include "improper_zero2.h"
#include "atom.h"
#include "error.h"
#include "memory.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ImproperZero2::ImproperZero2(LAMMPS *lmp) : Improper(lmp), coeffflag(1)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
ImproperZero2::~ImproperZero2()
{
if (allocated && !copymode) {
memory->destroy(setflag);
}
}
/* ---------------------------------------------------------------------- */
void ImproperZero2::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void ImproperZero2::settings(int narg, char **arg)
{
if ((narg != 0) && (narg != 1))
error->all(FLERR,"Illegal improper_style command");
if (narg == 1) {
if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
else error->all(FLERR,"Illegal improper_style command");
}
}
/* ---------------------------------------------------------------------- */
void ImproperZero2::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void ImproperZero2::coeff(int narg, char **arg)
{
if ((narg < 1) || (coeffflag && narg > 1))
error->all(FLERR,"Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nimpropertypes,ilo,ihi,error);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperZero2::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperZero2::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void ImproperZero2::write_data(FILE *fp) {
for (int i = 1; i <= atom->nimpropertypes; i++)
fprintf(fp,"%d\n",i);
}

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/* -*- 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_IMPROPER_ZERO2_H
#define LMP_IMPROPER_ZERO2_H
#include "improper.h"
namespace LAMMPS_NS {
class ImproperZero2 : public Improper {
public:
ImproperZero2(class LAMMPS *);
virtual ~ImproperZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
int coeffflag;
virtual void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for improper coefficients
Self-explanatory. Check the input script or data file.
*/

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#include "lammpsplugin.h"
#include "version.h"
#include <cstring>
#include "pair_morse2.h"
#include "pair_morse2_omp.h"
using namespace LAMMPS_NS;
static Pair *morse2creator(LAMMPS *lmp)
{
return new PairMorse2(lmp);
}
static Pair *morse2ompcreator(LAMMPS *lmp)
{
return new PairMorse2OMP(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register plain morse2 pair style
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "morse2";
plugin.info = "Morse2 variant pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
// also register morse2/omp pair style. only need to update changed fields
plugin.name = "morse2/omp";
plugin.info = "Morse2 variant pair style for OpenMP v1.0";
plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2ompcreator;
(*register_plugin)(&plugin,lmp);
}

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#include "lammpsplugin.h"
#include "version.h"
#include <cstring>
#include "fix_nve2.h"
using namespace LAMMPS_NS;
static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixNVE2(lmp, argc, argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "nve2";
plugin.info = "NVE2 variant fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
#include "pair_morse2.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMorse2::PairMorse2(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairMorse2::~PairMorse2()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(d0);
memory->destroy(alpha);
memory->destroy(r0);
memory->destroy(morse1);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairMorse2::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,dr,dexp,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairMorse2::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(d0,n+1,n+1,"pair:d0");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(r0,n+1,n+1,"pair:r0");
memory->create(morse1,n+1,n+1,"pair:morse1");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMorse2::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = utils::numeric(FLERR,arg[0],false,lmp);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMorse2::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
double d0_one = utils::numeric(FLERR,arg[2],false,lmp);
double alpha_one = utils::numeric(FLERR,arg[3],false,lmp);
double r0_one = utils::numeric(FLERR,arg[4],false,lmp);
double cut_one = cut_global;
if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
d0[i][j] = d0_one;
alpha[i][j] = alpha_one;
r0[i][j] = r0_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMorse2::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
if (offset_flag) {
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
} else offset[i][j] = 0.0;
d0[j][i] = d0[i][j];
alpha[j][i] = alpha[i][j];
r0[j][i] = r0[i][j];
morse1[j][i] = morse1[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMorse2::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&d0[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&r0[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMorse2::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMorse2::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMorse2::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairMorse2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairMorse2::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g %g\n",
i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
return factor_lj*phi;
}
/* ---------------------------------------------------------------------- */
void *PairMorse2::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"d0") == 0) return (void *) d0;
if (strcmp(str,"r0") == 0) return (void *) r0;
if (strcmp(str,"alpha") == 0) return (void *) alpha;
return nullptr;
}

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/* -*- 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_PAIR_MORSE2_H
#define LMP_PAIR_MORSE2_H
#include "pair.h"
namespace LAMMPS_NS {
class PairMorse2 : public Pair {
public:
PairMorse2(class LAMMPS *);
virtual ~PairMorse2();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
protected:
double cut_global;
double **cut;
double **d0,**alpha,**r0;
double **morse1;
double **offset;
virtual void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "pair_morse2_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "suffix.h"
#include <cmath>
#include "omp_compat.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMorse2OMP::PairMorse2OMP(LAMMPS *lmp) :
PairMorse2(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairMorse2OMP::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairMorse2OMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,dr,dexp,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}
/* ---------------------------------------------------------------------- */
double PairMorse2OMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairMorse2::memory_usage();
return bytes;
}

41
examples/plugins/pair_morse2_omp.h Normal file
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@ -0,0 +1,41 @@
/* -*- 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_MORSE2_OMP_H
#define LMP_PAIR_MORSE2_OMP_H
#include "pair_morse2.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
class PairMorse2OMP : public PairMorse2, public ThrOMP {
public:
PairMorse2OMP(class LAMMPS *);
virtual void compute(int, int);
virtual double memory_usage();
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void eval(int ifrom, int ito, ThrData * const thr);
};
}
#endif

247
examples/plugins/pair_zero2.cpp Normal file
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@ -0,0 +1,247 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
#include "pair_zero2.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairZero2::PairZero2(LAMMPS *lmp) : Pair(lmp) {
coeffflag=1;
writedata=1;
single_enable=1;
respa_enable=1;
}
/* ---------------------------------------------------------------------- */
PairZero2::~PairZero2()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
}
}
/* ---------------------------------------------------------------------- */
void PairZero2::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairZero2::compute_outer(int eflag, int vflag)
{
ev_init(eflag,vflag);
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairZero2::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairZero2::settings(int narg, char **arg)
{
if ((narg != 1) && (narg != 2))
error->all(FLERR,"Illegal pair_style command");
cut_global = utils::numeric(FLERR,arg[0],false,lmp);
if (narg == 2) {
if (strcmp("nocoeff",arg[1]) == 0) coeffflag=0;
else error->all(FLERR,"Illegal pair_style command");
}
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairZero2::coeff(int narg, char **arg)
{
if ((narg < 2) || (coeffflag && narg > 3))
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
double cut_one = cut_global;
if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR,arg[2],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairZero2::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairZero2::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairZero2::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairZero2::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&coeffflag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairZero2::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&coeffflag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairZero2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d\n",i);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairZero2::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g\n",i,j,cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairZero2::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */,
double /* rsq */, double /*factor_coul*/,
double /* factor_lj */, double &fforce)
{
fforce = 0.0;
return 0.0;
}

77
examples/plugins/pair_zero2.h Normal file
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@ -0,0 +1,77 @@
/* -*- 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.
Pair zero is a dummy pair interaction useful for requiring a
force cutoff distance in the absence of pair-interactions or
with hybrid/overlay if a larger force cutoff distance is required.
This can be used in conjunction with bond/create to create bonds
that are longer than the cutoff of a given force field, or to
calculate radial distribution functions for models without
pair interactions.
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_ZERO2_H
#define LMP_PAIR_ZERO2_H
#include "pair.h"
namespace LAMMPS_NS {
class PairZero2 : public Pair {
public:
PairZero2(class LAMMPS *);
virtual ~PairZero2();
virtual void compute(int, int);
virtual void compute_outer(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
protected:
double cut_global;
double **cut;
int coeffflag;
virtual void allocate();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
U: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
*/

78
examples/plugins/zero2plugin.cpp Normal file
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@ -0,0 +1,78 @@
#include "lammpsplugin.h"
#include "version.h"
#include <cstring>
#include "pair_zero2.h"
#include "bond_zero2.h"
#include "angle_zero2.h"
#include "dihedral_zero2.h"
#include "improper_zero2.h"
using namespace LAMMPS_NS;
static Pair *pairzerocreator(LAMMPS *lmp)
{
return new PairZero2(lmp);
}
static Bond *bondzerocreator(LAMMPS *lmp)
{
return new BondZero2(lmp);
}
static Angle *anglezerocreator(LAMMPS *lmp)
{
return new AngleZero2(lmp);
}
static Dihedral *dihedralzerocreator(LAMMPS *lmp)
{
return new DihedralZero2(lmp);
}
static Improper *improperzerocreator(LAMMPS *lmp)
{
return new ImproperZero2(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register zero2 pair style
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "zero2";
plugin.info = "Zero2 variant pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &pairzerocreator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
// register zero2 bond style
plugin.style = "bond";
plugin.info = "Zero2 variant bond style v1.0";
plugin.creator.v1 = (lammpsplugin_factory1 *) &bondzerocreator;
(*register_plugin)(&plugin,lmp);
// register zero2 angle style
plugin.style = "angle";
plugin.info = "Zero2 variant angle style v1.0";
plugin.creator.v1 = (lammpsplugin_factory1 *) &anglezerocreator;
(*register_plugin)(&plugin,lmp);
// register zero2 dihedral style
plugin.style = "dihedral";
plugin.info = "Zero2 variant dihedral style v1.0";
plugin.creator.v1 = (lammpsplugin_factory1 *) &dihedralzerocreator;
(*register_plugin)(&plugin,lmp);
// register zero2 improper style
plugin.style = "improper";
plugin.info = "Zero2 variant improper style v1.0";
plugin.creator.v1 = (lammpsplugin_factory1 *) &improperzerocreator;
(*register_plugin)(&plugin,lmp);
}

20
lib/README
View File

@ -19,12 +19,12 @@ atc atomistic-to-continuum methods, USER-ATC package
from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia)
awpmd antisymmetrized wave packet molecular dynamics, AWPMD package
from Ilya Valuev (JIHT RAS)
colvars collective variable module (Metadynamics, ABF and more)
colvars collective variable module (Metadynamics, ABF and more)
from Giacomo Fiorin and Jerome Henin (ICMS, Temple U)
compress hook to system lib for performing I/O compression, COMPRESS pkg
from Axel Kohlmeyer (Temple U)
gpu general GPU routines, GPU package
from Mike Brown (ORNL)
from Axel Kohlmeyer (Temple U)
gpu general GPU routines, GPU package
from Mike Brown (ORNL)
h5md ch5md library for output of MD data in HDF5 format
from Pierre de Buyl (KU Leuven)
kim hooks to the KIM library, used by KIM package
@ -32,26 +32,28 @@ kim hooks to the KIM library, used by KIM package
kokkos Kokkos package for GPU and many-core acceleration
from Kokkos development team (Sandia)
linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
from Axel Kohlmeyer (Temple U)
message client/server communication library via MPI, sockets, files
from Steve Plimpton (Sandia)
from Steve Plimpton (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
from Jacob Wagner and Greg Voth group (U Chicago)
netcdf hooks to a NetCDF library installed on your system
from Lars Pastewka (Karlsruhe Institute of Technology)
poems POEMS rigid-body integration package, POEMS package
plugin settings to load styles into LAMMPS from plugins
from Axel Kohlmeyer (Temple U)
poems POEMS rigid-body integration package, POEMS package
from Rudranarayan Mukherjee (RPI)
python hooks to the system Python library, used by the PYTHON package
from the LAMMPS development team
qmmm quantum mechanics/molecular mechanics coupling interface
qmmm quantum mechanics/molecular mechanics coupling interface
from Axel Kohlmeyer (Temple U)
quip interface to QUIP/libAtoms framework, USER-QUIP package
from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
smd hooks to Eigen library, used by USER-SMD package
from Georg Ganzenmueller (Ernst Mach Institute, Germany)
voronoi hooks to the Voro++ library, used by compute voronoi/atom command
from Daniel Schwen (LANL)
from Daniel Schwen (LANL)
vtk hooks to the VTK library, used by dump custom/vtk command
from Richard Berger (JKU)

6
lib/gpu/Makefile.hip
View File

@ -1,6 +1,6 @@
# /* ----------------------------------------------------------------------
# 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
# ------------------------------------------------------------------------- */
@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (amd,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (nvcc,$(HIP_PLATFORM))
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] \

5
lib/gpu/README
View File

@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and
extract the cub directory to lammps/lib/gpu/ or specify an appropriate
path in lammps/lib/gpu/Makefile.hip.
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
architecture (gfx803, gfx900, gfx906 etc.)
export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0)
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,
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.
@ -278,4 +278,3 @@ and
Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High
Performance Computers - Three-Body Potentials. Computer Physics Communications.
2013. 184: p. 2785–2793.

1
lib/gpu/lal_neighbor.cpp
View File

@ -740,6 +740,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
// If binning on GPU, do this now
if (_gpu_nbor==1) {
mn = _max_nbors;
const numtyp i_cell_size=static_cast<numtyp>(1.0/_cell_size);
const int neigh_block=_block_cell_id;
const int GX=(int)ceil((float)nall/neigh_block);

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