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Merge branch 'develop' into BPM

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This commit is contained in:
jtclemm
2022-01-12 10:52:11 -07:00
committed by GitHub
parent 744e615dbb 878557dd48
commit 19abc5d329
884 changed files with 39864 additions and 18216 deletions
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4
SECURITY.md
View File

@ -23,6 +23,10 @@ either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide
malicious changes to the source code, all LAMMPS submissions are checked
for unicode characters and only all-ASCII source code is accepted.
# Version Updates

20
cmake/CMakeLists.txt
View File

@ -133,10 +133,7 @@ endif()
set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
@ -304,10 +301,12 @@ else()
target_link_libraries(lmp PRIVATE mpi_stubs)
target_include_directories(lmp INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lmp INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
endif(MSVC)
endif()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
else()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
add_library(MPI::MPI_CXX ALIAS mpi_stubs)
@ -341,7 +340,6 @@ pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
@ -611,7 +609,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -810,11 +808,17 @@ if(ClangFormat_FOUND)
endif()
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(BUILD_IS_MULTI_CONFIG)
set(LAMMPS_BUILD_TYPE "Multi-Config")
else()
set(LAMMPS_BUILD_TYPE ${CMAKE_BUILD_TYPE})
endif()
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
message(STATUS "<<< Build configuration >>>
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
Build type: ${CMAKE_BUILD_TYPE}
Build type: ${LAMMPS_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
###############################################################################

154
cmake/CMakeSettings.json
View File

@ -1,55 +1,111 @@
{
"configurations": [
"configurations": [
{
"name": "x64-Debug-MSVC",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "x64-Debug-MSVC",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "x64-Debug-Clang",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
]
},
{
"name": "x64-Debug-Clang",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-OneAPI",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-Intel",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=off -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
}
]
}

33
cmake/Modules/ExternalCMakeProject.cmake Normal file
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@ -0,0 +1,33 @@
# Build a CMake based external library as subdirectory.
# The sources will be unpacked to ${CMAKE_BINARY_DIR}/_deps/${target}-src
# The binaries will be built in ${CMAKE_BINARY_DIR}/_deps/${target}-build
#
function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
# change settings locally
set(BUILD_SHARED_LIBS OFF)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
get_filename_component(archive ${url} NAME)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
message(STATUS "Unpacking and configuring ${archive}")
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
file(GLOB TARGET_SOURCE "${CMAKE_BINARY_DIR}/_deps/src/${basedir}*")
list(LENGTH TARGET_SOURCE _num)
if(_num GREATER 1)
message(FATAL_ERROR "Inconsistent ${target} library sources. "
"Please delete ${CMAKE_BINARY_DIR}/_deps/src and re-run cmake")
endif()
file(REMOVE_RECURSE ${CMAKE_BINARY_DIR}/_deps/${target}-src)
file(RENAME ${TARGET_SOURCE} ${CMAKE_BINARY_DIR}/_deps/${target}-src)
if(NOT (cmakefile STREQUAL ""))
file(COPY ${cmakefile} DESTINATION ${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/)
get_filename_component(_cmakefile ${cmakefile} NAME)
file(RENAME "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/${_cmakefile}"
"${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
endif()
add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
"${CMAKE_BINARY_DIR}/_deps/${target}-build")
endfunction(ExternalCMakeProject)

81
cmake/Modules/GTest.cmake
View File

@ -1,81 +0,0 @@
message(STATUS "Downloading and building Google Test library")
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
set(GTEST_LIB_POSTFIX d)
else()
set(GTEST_LIB_POSTFIX)
endif()
include(ExternalProject)
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.11.0.tar.gz" CACHE STRING "URL of googletest source")
set(GTEST_MD5 "e8a8df240b6938bb6384155d4c37d937" CACHE STRING "MD5 sum for googletest source")
mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
ExternalProject_Add(googletest
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} ${CMAKE_EXTRA_GTEST_OPTS}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Get_Property(googletest SOURCE_DIR)
set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
ExternalProject_Get_Property(googletest BINARY_DIR)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
# Prevent GoogleTest from overriding our compiler/linker options
# when building with Visual Studio
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
find_package(Threads QUIET)
add_library(GTest::GTest UNKNOWN IMPORTED)
set_target_properties(GTest::GTest PROPERTIES
IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GTest googletest)
add_library(GTest::GMock UNKNOWN IMPORTED)
set_target_properties(GTest::GMock PROPERTIES
IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GMock googletest)
add_library(GTest::GTestMain UNKNOWN IMPORTED)
set_target_properties(GTest::GTestMain PROPERTIES
IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GTestMain googletest)
add_library(GTest::GMockMain UNKNOWN IMPORTED)
set_target_properties(GTest::GMockMain PROPERTIES
IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GMockMain googletest)

2
cmake/Modules/LAMMPSUtils.cmake
View File

@ -25,7 +25,7 @@ function(validate_option name values)
endfunction(validate_option)
function(get_lammps_version version_header variable)
file(READ ${version_header} line)
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")

4
cmake/Modules/Packages/GPU.cmake
View File

@ -306,12 +306,12 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()

6
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -39,8 +39,8 @@ 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/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.5.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "079323d973ae0e1c38c0a54a150c674e" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -60,7 +60,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.4.01 REQUIRED CONFIG)
find_package(Kokkos 3.5.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()

3
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -32,7 +32,8 @@ if(DOWNLOAD_QUIP)
foreach(flag ${LAPACK_LIBRARIES})
set(temp "${temp} ${flag}")
endforeach()
set(temp "${temp}\n")
# Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
set(temp "${temp} -L/_DUMMY_PATH_\n")
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")

39
cmake/Modules/Packages/MSCG.cmake
View File

@ -12,41 +12,12 @@ if(DOWNLOAD_MSCG)
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded MSCG library due to a technical limitation")
endif()
include(ExternalCMakeProject)
ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
include(ExternalProject)
ExternalProject_Add(mscg_build
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}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
)
ExternalProject_get_property(mscg_build BINARY_DIR)
ExternalProject_get_property(mscg_build SOURCE_DIR)
file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
add_library(LAMMPS::MSCG UNKNOWN IMPORTED)
set_target_properties(LAMMPS::MSCG PROPERTIES
IMPORTED_LOCATION "${BINARY_DIR}/libmscg.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
add_dependencies(LAMMPS::MSCG mscg_build)
# set include and link library
target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
target_link_libraries(lammps PRIVATE mscg)
else()
find_package(MSCG)
if(NOT MSCG_FOUND)

9
cmake/Modules/Packages/PHONON.cmake Normal file
View File

@ -0,0 +1,9 @@
# fix phonon may only be installed if also the FFT wrappers from KSPACE are installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

4
cmake/Modules/Packages/PLUMED.cmake
View File

@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.3/plumed-src-2.7.3.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "f00cc82edfefe6bb3df934911dbe32fb" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

47
cmake/Modules/YAML.cmake
View File

@ -1,47 +0,0 @@
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)
# support cross-compilation to windows
if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
set(YAML_CROSS_HOST --host=i686-mingw64)
elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(YAML_CROSS_HOST --host=x86_64-mingw64)
else()
message(FATAL_ERROR "Unsupported cross-compilation "
" for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
" on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
endif()
endif()
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")
ExternalProject_Get_Property(libyaml INSTALL_DIR)
set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
add_library(Yaml::Yaml UNKNOWN IMPORTED)
set_target_properties(Yaml::Yaml PROPERTIES
IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
add_dependencies(Yaml::Yaml libyaml)

1
cmake/presets/most.cmake
View File

@ -48,7 +48,6 @@ set(ALL_PACKAGES
PHONON
PLUGIN
POEMS
PYTHON
QEQ
REACTION
REAXFF

2
doc/Makefile
View File

@ -230,7 +230,7 @@ $(VENV):
)
$(MATHJAX):
@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
$(ANCHORCHECK): $(VENV)
@( \

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "1" "27 October 2021" "2021-10-27"
.TH LAMMPS "1" "7 January 2022" "2022-1-7"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

5
doc/src/Bibliography.rst
View File

@ -1123,9 +1123,12 @@ Bibliography
**(Sun)**
Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Surblys)**
**(Surblys2019)**
Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2021)**
Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
**(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)

36
doc/src/Build_cmake.rst
View File

@ -150,6 +150,42 @@ for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
.. _cmake_multiconfig:
Multi-configuration build systems
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Throughout this manual it is mostly assumed that LAMMPS is being built
on a Unix-like operating system with "make" as the underlying "builder",
since this is the most common case. In this case the build "configuration"
is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
Some build tools, however, can also use or even require to have a so-called
multi-configuration build system setup. For those the built type (or
configuration) is chosen at compile time using the same build files. E.g.
with:
.. code-block:: bash
cmake --build build-multi --config Release
In that case the resulting binaries are not in the build folder directly
but in sub-directories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag:
.. code-block:: bash
ctest -C Debug
The CMake scripts in LAMMPS have basic support for being compiled using a
multi-config build system, but not all of it has been ported. This is in
particular applicable to compiling packages that require additional libraries
that would be downloaded and compiled by CMake. The "windows" preset file
tries to keep track of which packages can be compiled natively with the
MSVC compilers out-of-the box. Not all of those external libraries are
portable to Windows either.
Installing CMake
^^^^^^^^^^^^^^^^

10
doc/src/Build_development.rst
View File

@ -185,6 +185,10 @@ The ``ctest`` command has many options, the most important ones are:
- run subset of tests matching the regular expression <regex>
* - -E <regex>
- exclude subset of tests matching the regular expression <regex>
* - -L <regex>
- run subset of tests with a label matching the regular expression <regex>
* - -LE <regex>
- exclude subset of tests with a label matching the regular expression <regex>
* - -N
- dry-run: display list of tests without running them
* - -T memcheck
@ -299,6 +303,12 @@ will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
and working.
Some of the force style tests are rather slow to run and some are very
sensitive to small differences like CPU architecture, compiler
toolchain, compiler optimization. Those tests are flagged with a "slow"
and/or "unstable" label, and thus those tests can be selectively
excluded with the ``-LE`` flag or selected with the ``-L`` flag.
.. admonition:: Recommendations and notes for YAML files
:class: note

33
doc/src/Build_extras.rst
View File

@ -341,6 +341,18 @@ minutes to hours) to build. Of course you only need to do that once.)
$ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
When using the "-b " option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be
provided on the command line for use by cmake. For example, to use the
``cmake3`` executable and tell it to use the gnu version 11 compilers
to build KIM, one could use the following command line.
.. code-block:: bash
$ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through
editing the ``Makefile.machine`` you are using. For example:
@ -560,11 +572,26 @@ They must be specified in uppercase.
* - VEGA908
- GPU
- AMD GPU MI100 GFX908
* - INTEL_GEN
* - VEGA90A
- GPU
- Intel GPUs Gen9+
- AMD GPU
* - INTEL_DG1
- GPU
- Intel Iris XeMAX GPU
* - INTEL_GEN9
- GPU
- Intel GPU Gen9
* - INTEL_GEN11
- GPU
- Intel GPU Gen11
* - INTEL_GEN12LP
- GPU
- Intel GPU Gen12LP
* - INTEL_XEHP
- GPU
- Intel GPUs Xe-HP
This list was last updated for version 3.4.1 of the Kokkos library.
This list was last updated for version 3.5.0 of the Kokkos library.
.. tabs::

5
doc/src/Build_windows.rst
View File

@ -89,6 +89,11 @@ miss the correct master ``CMakeLists.txt``. Try to open the
starting point. It is also possible to configure and compile LAMMPS
from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
Please note, that for either approach CMake will create a so-called
:ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
the command lines for building and testing LAMMPS must be adjusted
accordingly.
To support running in parallel you can compile with OpenMP enabled using
the OPENMP package or install Microsoft MPI (including the SDK) and compile
LAMMPS with MPI enabled.

1
doc/src/Commands_bond.rst
View File

@ -37,6 +37,7 @@ OPT.
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`fene/nm <bond_fene>`
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`

1
doc/src/Commands_compute.rst
View File

@ -28,6 +28,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`angle <compute_angle>`
* :doc:`angle/local <compute_angle_local>`
* :doc:`angmom/chunk <compute_angmom_chunk>`
* :doc:`ave/sphere/atom (k) <compute_ave_sphere_atom>`
* :doc:`basal/atom <compute_basal_atom>`
* :doc:`body/local <compute_body_local>`
* :doc:`bond <compute_bond>`

2
doc/src/Commands_pair.rst
View File

@ -210,6 +210,7 @@ OPT.
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`
* :doc:`nm/cut/split <pair_nm>`
* :doc:`oxdna/coaxstk <pair_oxdna>`
* :doc:`oxdna/excv <pair_oxdna>`
* :doc:`oxdna/hbond <pair_oxdna>`
@ -262,6 +263,7 @@ OPT.
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/mod (o) <pair_sw>`
* :doc:`table (gko) <pair_table>`
* :doc:`table/rx (k) <pair_table_rx>`
* :doc:`tdpd <pair_mesodpd>`

3
doc/src/Developer_platform.rst
View File

@ -118,6 +118,9 @@ Environment variable functions
.. doxygenfunction:: putenv
:project: progguide
.. doxygenfunction:: unsetenv
:project: progguide
.. doxygenfunction:: list_pathenv
:project: progguide

31
doc/src/Developer_utils.rst
View File

@ -56,11 +56,11 @@ String to number conversions with validity check
These functions should be used to convert strings to numbers. They are
are strongly preferred over C library calls like ``atoi()`` or
``atof()`` since they check if the **entire** provided string is a valid
``atof()`` since they check if the **entire** string is a valid
(floating-point or integer) number, and will error out instead of
silently returning the result of a partial conversion or zero in cases
where the string is not a valid number. This behavior allows to more
easily detect typos or issues when processing input files.
where the string is not a valid number. This behavior improves
detecting typos or issues when processing input files.
Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
will convert a string into a boolean and will only accept certain words.
@ -76,19 +76,34 @@ strings for compliance without conversion.
----------
.. doxygenfunction:: numeric
.. doxygenfunction:: numeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: inumeric
.. doxygenfunction:: numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical
.. doxygenfunction:: bnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide

2
doc/src/Developer_write.rst
View File

@ -55,7 +55,7 @@ of each timestep. First of all, implement a constructor:
if (narg < 4)
error->all(FLERR,"Illegal fix print/vel command");
nevery = force->inumeric(FLERR,arg[3]);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0)
error->all(FLERR,"Illegal fix print/vel command");
}

3
doc/src/Errors_messages.rst
View File

@ -7772,9 +7772,6 @@ keyword to allow for additional bonds to be formed
The system size must fit in a 32-bit integer to use this dump
style.
*Too many atoms to dump sort*
Cannot sort when running with more than 2\^31 atoms.
*Too many elements extracted from MEAM library.*
Increase 'maxelt' in meam.h and recompile.

5
doc/src/Howto_drude2.rst
View File

@ -491,11 +491,6 @@ NPT ensemble using Nose-Hoover thermostat:
**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133,
154511 (2010).
.. _Jiang2:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
J Phys Chem Lett, 2, 87-92 (2011).
.. _Thole2:
**(Thole)** Chem Phys, 59, 341 (1981).

3
doc/src/Howto_github.rst
View File

@ -141,7 +141,8 @@ unrelated feature, you should switch branches!
Committing changes to the *develop*, *release*, or *stable* branches
is strongly discouraged. While it may be convenient initially, it
will create more work in the long run. Various texts and tutorials
on using git effectively discuss the motivation for this.
on using git effectively discuss the motivation for using feature
branches instead.
**After changes are made**

35
doc/src/Install_git.rst
View File

@ -28,8 +28,9 @@ provides `limited support for subversion clients <svn_>`_.
You can follow the LAMMPS development on 3 different git branches:
* **stable** : this branch is updated with every stable release;
updates are always "fast forward" merges from *develop*
* **stable** : this branch is updated from the *release* branch with
every stable release version and also has selected bug fixes and updates
back-ported from the *develop* branch
* **release** : this branch is updated with every patch release;
updates are always "fast forward" merges from *develop*
* **develop** : this branch follows the ongoing development and
@ -47,20 +48,22 @@ your machine and "release" is one of the 3 branches listed above.
(Note that you actually download all 3 branches; you can switch
between them at any time using "git checkout <branch name>".)
.. note::
.. admonition:: Saving time and disk space when using ``git clone``
The complete git history of the LAMMPS project is quite large because
it contains the entire commit history of the project since fall 2006,
which includes the time when LAMMPS was managed with subversion. This
also includes commits that have added and removed some large files
(mostly by accident). If you do not need access to the entire commit
history, you can speed up the "cloning" process and reduce local disk
space requirements by using the *--depth* git command line flag thus
create a "shallow clone" of the repository that contains only a
subset of the git history. Using a depth of 1000 is usually sufficient
to include the head commits of the *develop* and the *release* branches.
To include the head commit of the *stable* branch you may need a depth
of up to 10000.
which includes the time when LAMMPS was managed with subversion.
This includes a few commits that have added and removed some large
files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the
*--depth* git command line flag. That will create a "shallow clone"
of the repository containing only a subset of the git history. Using
a depth of 1000 is usually sufficient to include the head commits of
the *develop* and the *release* branches. To include the head commit
of the *stable* branch you may need a depth of up to 10000. If you
later need more of the git history, you can always convert the
shallow clone into a "full clone".
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with the exception, that
@ -156,9 +159,9 @@ changed. How to do this depends on the build system you are using.
.. 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
The servers at github.com support the "https://" access protocol 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

2
doc/src/Intro_citing.rst
View File

@ -16,7 +16,7 @@ source code design, the program structure, the spatial decomposition
approach, the neighbor finding, basic communications algorithms, and how
users and developers have contributed to LAMMPS is:
`LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. (accepted 09/2021), DOI:10.1016/j.cpc.2021.108171 <https://doi.org/10.1016/j.cpc.2021.108171>`_
`LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. 271, 108171 (2022) <https://doi.org/10.1016/j.cpc.2021.108171>`_
So a project using LAMMPS or a derivative application that uses LAMMPS
as a simulation engine should cite this paper. The paper is expected to

24
doc/src/Manual_version.rst
View File

@ -10,23 +10,31 @@ Whenever we fix a bug or update or add a feature, it will be merged into
the *develop* branch of the git repository. When a sufficient number of
changes have accumulated *and* the software passes a set of automated
tests, we release it in the next *patch* release, which are made every
few weeks. Info on patch releases are on `this website page
few weeks. The *release* branch of the git repository is updated with
every such release. Info on patch releases are on `this website page
<https://www.lammps.org/bug.html>`_.
Once or twice a year, only bug fixes and small, non-intrusive changes are
included for a period of time, and the code is subjected to more detailed
Once or twice a year, we apply only bug fixes and small, non-intrusive
changes to the *develop* branch and the code is subjected to more detailed
and thorough testing than the default automated testing. The latest
patch release after such a period is then labeled as a *stable* version.
patch release after such a period is then also labeled as a *stable* version
and the *stable* branch is updated with it. Between stable releases
we occasionally release some updates to the stable release containing
only bug fixes and updates back-ported from *develop* but no new features
and update the *stable* branch accordingly.
Each version of LAMMPS contains all the features and bug-fixes up to
and including its version date.
Each version of LAMMPS contains all the documented features up to and
including its version date.
The version date is printed to the screen and logfile every time you
run LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball. And it is on the
first page of the :doc:`manual <Manual>`.
* If you browse the HTML pages on the LAMMPS WWW site, they always
describe the most current patch release of LAMMPS.
* If you browse the HTML pages on the LAMMPS WWW site, they will by
default describe the most current patch release version of LAMMPS.
In the navigation bar on the bottom left, there is the option to
view instead the documentation for the most recent *stable* version
or the latest version from the current development branch.
* If you browse the HTML pages included in your tarball, they
describe the version you have, which may be older.

38
doc/src/Modify_pair.rst
View File

@ -12,24 +12,24 @@ includes some optional methods to enable its use with rRESPA.
Here is a brief description of the class methods in pair.h:
+---------------------------------+-------------------------------------------------------------------+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+-------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
+---------------------------------+-------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+-------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+-------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+-------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+-------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+-------------------------------------------------------------------+
| single | force and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+-------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+-------------------------------------------------------------------+
+---------------------------------+---------------------------------------------------------------------+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+---------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
+---------------------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+---------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+---------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+---------------------------------------------------------------------+
The inner/middle/outer routines are optional.

6
doc/src/Packages_details.rst
View File

@ -1907,6 +1907,12 @@ MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.

38
doc/src/angle_class2.rst
View File

@ -64,34 +64,44 @@ These are the 4 coefficients for the :math:`E_a` formula:
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 4 coefficients, the
first of which is "bb" to indicate they are BondBond coefficients. In
a data file, these coefficients should be listed under a "BondBond
Coeffs" heading and you must leave out the "bb", i.e. only list 3
coefficients after the angle type.
* bb
* :math:`M` (energy/distance\^2)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 5 coefficients, the
first of which is "ba" to indicate they are BondAngle coefficients.
In a data file, these coefficients should be listed under a "BondAngle
Coeffs" heading and you must leave out the "ba", i.e. only list 4
coefficients after the angle type.
* ba
* :math:`N_1` (energy/distance\^2)
* :math:`N_2` (energy/distance\^2)
* :math:`N_1` (energy/distance)
* :math:`N_2` (energy/distance)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
.. note::
It is important that the order of the I,J,K atoms in each angle
listed in the Angles section of the data file read by the
:doc:`read_data <read_data>` command be consistent with the order
of the :math:`r_1` and :math:`r_2` BondBond and BondAngle
coefficients. This is because the terms in the formulas for
:math:`E_{bb}` and :math:`E_{ba}` will use the I,J atoms to compute
:math:`r_{ij}` and the J,K atoms to compute :math:`r_{jk}`.
----------
.. include:: accel_styles.rst

46
doc/src/bond_fene.rst
View File

@ -1,4 +1,5 @@
.. index:: bond_style fene
.. index:: bond_style fene/nm
.. index:: bond_style fene/intel
.. index:: bond_style fene/kk
.. index:: bond_style fene/omp
@ -8,12 +9,16 @@ bond_style fene command
Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
bond_style fene/nm command
==========================
Syntax
""""""
.. code-block:: LAMMPS
bond_style fene
bond_style fene/nm
Examples
""""""""
@ -23,6 +28,9 @@ Examples
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_style fene/nm
bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
Description
"""""""""""
@ -38,16 +46,36 @@ term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
The *fene/nm* bond style substitutes the standard LJ potential with the generalized LJ potential
in the same form as in pair style :doc:`nm/cut <pair_nm>`. The bond energy is then given by
.. math::
E = -0.5 K r_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
Similar to the *fene* style, the generalized Lennard-Jones is cut off at
the potential minimum, :math:`r_0`, to be repulsive only. The following
coefficients must be defined for each bond type via the :doc:`bond_coeff
<bond_coeff>` command as in the example 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:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
For the *fene/nm* style, the following coefficients are used. Please
note, that the standard LJ potential and thus the regular FENE potential
is recovered for (n=12 m=6) and :math:`r_0 = 2^\frac{1}{6} \sigma`.
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`E_0` (energy)
* :math:`r_0` (distance)
* :math:`n` (unitless)
* :math:`m` (unitless)
----------
.. include:: accel_styles.rst
@ -57,9 +85,10 @@ or :doc:`read_restart <read_restart>` commands:
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the :doc:`Build package <Build_package>` page for more
info.
The *fene* bond style can only be used if LAMMPS was built with the MOLECULE
package; the *fene/nm* bond style can only be used if LAMMPS was built
with the EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
page for more info.
You typically should specify :doc:`special_bonds fene <special_bonds>`
or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
@ -68,7 +97,8 @@ style. LAMMPS will issue a warning it that's not the case.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`pair style lj/cut <pair_lj>`, :doc:`pair style nm/cut <pair_nm>`.
Default
"""""""

1
doc/src/bond_style.rst
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@ -87,6 +87,7 @@ accelerated styles exist.
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
* :doc:`fene/nm <bond_fene>` - FENE bonds with a generalized Lennard-Jones potential
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond

1
doc/src/compute.rst
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@ -174,6 +174,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`angle <compute_angle>` - energy of each angle sub-style
* :doc:`angle/local <compute_angle_local>` - theta and energy of each angle
* :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
* :doc:`ave/sphere/atom <compute_ave_sphere_atom>` - compute local density and temperature around each atom
* :doc:`basal/atom <compute_basal_atom>` - calculates the hexagonal close-packed "c" lattice vector of each atom
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
* :doc:`bond <compute_bond>` - energy of each bond sub-style

101
doc/src/compute_ave_sphere_atom.rst Normal file
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@ -0,0 +1,101 @@
.. index:: compute ave/sphere/atom
.. index:: compute ave/sphere/atom/kk
compute ave/sphere/atom command
================================
Accelerator Variants: *ave/sphere/atom/kk*
Syntax
""""""
.. parsed-literal::
compute ID group-ID ave/sphere/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* ave/sphere/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all ave/sphere/atom
compute 1 all ave/sphere/atom cutoff 5.0
comm_modify cutoff 5.0
Description
"""""""""""
Define a computation that calculates the local density and temperature
for each atom and neighbors inside a spherical cutoff.
The optional keyword *cutoff* defines the distance cutoff
used when searching for neighbors. The default value is the cutoff
specified by the pair style. If no pair style is defined, then a cutoff
must be defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is defined),
the *comm_modify cutoff* option must also be set to match that of the
*cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
:doc:`rerun <rerun>` command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""
This compute calculates a per-atom array with two columns: density and temperature.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff

6
doc/src/compute_bond_local.rst
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@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* bond/local = style name of this compute command
* one or more values may be appended
* value = *dist* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
.. parsed-literal::
@ -21,6 +21,7 @@ Syntax
*engpot* = bond potential energy
*force* = bond force
*dx*,\ *dy*,\ *dz* = components of pairwise distance
*fx*,\ *fy*,\ *fz* = components of bond force
*engvib* = bond kinetic energy of vibration
*engrot* = bond kinetic energy of rotation
@ -63,6 +64,9 @@ whether the 2 atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value *dist* is the current length of the bond.
The values *dx*, *dy*, and *dz* are the xyz components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of lower to the one with the higher id.
The value *engpot* is the potential energy for the bond,
based on the current separation of the pair of atoms in the bond.

21
doc/src/compute_heat_flux.rst
View File

@ -89,13 +89,20 @@ included in the calculation.
.. warning::
The compute *heat/flux* has been reported to produce unphysical
values for angle, dihedral and improper contributions
values for angle, dihedral, improper and constraint force contributions
when used with :doc:`compute stress/atom <compute_stress_atom>`,
as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
You are strongly advised to
as discussed in :ref:`(Surblys2019) <Surblys3>`, :ref:`(Boone) <Boone>`
and :ref:`(Surblys2021) <Surblys4>`. You are strongly advised to
use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
which has been implemented specifically for such cases.
.. warning::
Due to an implementation detail, the :math:`y` and :math:`z`
components of heat flux from :doc:`fix rigid <fix_rigid>`
contribution when computed via :doc:`compute stress/atom <compute_stress_atom>`
are highly unphysical and should not be used.
The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux :math:`\mathbf{J}`
to the thermal conductivity :math:`\kappa`:
@ -232,10 +239,14 @@ none
----------
.. _Surblys2:
.. _Surblys3:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _Boone:
**(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
.. _Surblys4:
**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).

14
doc/src/compute_pair_local.rst
View File

@ -13,11 +13,12 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* pair/local = style name of this compute command
* one or more values may be appended
* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
* value = *dist* or *dx* or *dy* or *dz* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
.. parsed-literal::
*dist* = pairwise distance
*dx*,\ *dy*,\ *dz* = components of pairwise distance
*eng* = pairwise energy
*force* = pairwise force
*fx*,\ *fy*,\ *fz* = components of pairwise force
@ -56,6 +57,9 @@ force cutoff distance for that interaction, as defined by the
commands.
The value *dist* is the distance between the pair of atoms.
The values *dx*, *dy*, and *dz* are the xyz components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of lower to the one with the higher id.
The value *eng* is the interaction energy for the pair of atoms.
@ -89,10 +93,10 @@ from the second of the two sub-styles. If the referenced *pN*
is not computed for the specific pairwise interaction (based on
atom types), then the output will be 0.0.
The value *dist* will be in distance :doc:`units <units>`. The value
*eng* will be in energy :doc:`units <units>`. The values *force*, *fx*,
*fy*, and *fz* will be in force :doc:`units <units>`. The values *pN*
will be in whatever units the pair style defines.
The value *dist*, *dx*, *dy* and *dz* will be in distance :doc:`units <units>`.
The value *eng* will be in energy :doc:`units <units>`.
The values *force*, *fx*, *fy*, and *fz* will be in force :doc:`units <units>`.
The values *pN* will be in whatever units the pair style defines.
The optional *cutoff* keyword determines how the force cutoff distance
for an interaction is determined. For the default setting of *type*,

45
doc/src/compute_stress_atom.rst
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@ -87,6 +87,10 @@ Tersoff 3-body interaction) is assigned in equal portions to each atom
in the set. E.g. 1/4 of the dihedral virial to each of the 4 atoms,
or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
a water molecule via the :doc:`fix shake <fix_shake>` command.
As an exception, the virial contribution from
constraint forces in :doc:`fix rigid <fix_rigid>` on each atom
is computed from the constraint force acting on the corresponding atom
and its position, i.e. the total virial is not equally distributed.
In case of compute *centroid/stress/atom*, the virial contribution is:
@ -103,13 +107,25 @@ atom :math:`I` due to the interaction and the relative position
:math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
of the interacting atoms, i.e. centroid, is used. As the geometric
center is different for each interaction, the :math:`\mathbf{r}_{I0}`
also differs. The sixth and seventh terms, Kspace and :doc:`fix
<fix>` contribution respectively, are computed identical to compute
*stress/atom*. Although the total system virial is the same as
also differs. The sixth term, Kspace contribution,
is computed identically to compute *stress/atom*.
The seventh term is handed differently depending on
if the constraint forces are due to :doc:`fix shake <fix_shake>`
or :doc:`fix rigid <fix_rigid>`.
In case of SHAKE constraints, each distance constraint is
handed as a pairwise interaction.
E.g. in case of a water molecule, two OH and one HH distance
constraints are treated as three pairwise interactions.
In case of :doc:`fix rigid <fix_rigid>`,
all constraint forces in the molecule are treated
as a single many-body interaction with a single centroid position.
In case of water molecule, the formula expression would become
identical to that of the three-body angle interaction.
Although the total system virial is the same as
compute *stress/atom*, compute *centroid/stress/atom* is know to
result in more consistent heat flux values for angle, dihedrals and
improper contributions when computed via :doc:`compute heat/flux
<compute_heat_flux>`.
result in more consistent heat flux values for angle, dihedrals,
improper and constraint force contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution all of the
virial contribution terms are included in the per-atom stress tensor.
@ -134,7 +150,8 @@ contribution for the cluster interaction is divided evenly among those
atoms.
Details of how compute *centroid/stress/atom* obtains the virial for
individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
individual atoms are given in :ref:`(Surblys2019) <Surblys1>` and
:ref:`(Surblys2021) <Surblys2>`, where the
idea is that the virial of the atom :math:`I` is the result of only
the force :math:`\mathbf{F}_I` on the atom due to the interaction and
its positional vector :math:`\mathbf{r}_{I0}`, relative to the
@ -235,10 +252,10 @@ between the pair of particles. All bond styles are supported. All
angle, dihedral, improper styles are supported with the exception of
INTEL and KOKKOS variants of specific styles. It also does not
support models with long-range Coulombic or dispersion forces,
i.e. the kspace_style command in LAMMPS. It also does not support the
following fixes which add rigid-body constraints: :doc:`fix shake
<fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
i.e. the kspace_style command in LAMMPS. It also does not implement the
following fixes which add rigid-body constraints:
:doc:`fix rigid/* <fix_rigid>` and the OpenMP accelerated version of :doc:`fix rigid/small <fix_rigid>`,
while all other :doc:`fix rigid/*/small <fix_rigid>` are implemented.
LAMMPS will generate an error if one of these options is included in
your model. Extension of centroid stress calculations to these force
@ -270,4 +287,8 @@ none
.. _Surblys1:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _Surblys2:
**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).

46
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@ -20,8 +20,10 @@ Syntax
cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
group1-ID = one atom in pair must be in this group
group2-ID = other atom in pair must be in this group
*porosity* args = region-ID fraction seed
*porosity* args = group-ID region-ID fraction seed
group-ID = group within which to perform deletions
region-ID = region within which to perform deletions
or NULL to only impose the group criterion
fraction = delete this fraction of atoms
seed = random number seed (positive integer)
@ -43,7 +45,8 @@ Examples
delete_atoms region sphere compress no
delete_atoms overlap 0.3 all all
delete_atoms overlap 0.5 solvent colloid
delete_atoms porosity cube 0.1 482793 bond yes
delete_atoms porosity all cube 0.1 482793 bond yes
delete_atoms porosity polymer cube 0.1 482793 bond yes
Description
"""""""""""
@ -76,12 +79,17 @@ have occurred that no atom pairs within the cutoff will remain
minimum number of atoms will be deleted, or that the same atoms will
be deleted when running on different numbers of processors.
For style *porosity* a specified *fraction* of atoms are deleted
within the specified region. For example, if fraction is 0.1, then
10% of the atoms will be deleted. The atoms to delete are chosen
randomly. There is no guarantee that the exact fraction of atoms will
be deleted, or that the same atoms will be deleted when running on
different numbers of processors.
For style *porosity* a specified *fraction* of atoms are deleted which
are both in the specified group and within the specified region. The
region-ID can be specified as NULL to only impose the group criterion.
Likewise, specifying the group-ID as *all* will only impose the region
criterion.
For example, if fraction is 0.1, then 10% of the eligible atoms will
be deleted. The atoms to delete are chosen randomly. There is no
guarantee that the exact fraction of atoms will be deleted, or that
the same atoms will be deleted when running on different numbers of
processors.
If the *compress* keyword is set to *yes*, then after atoms are
deleted, then atom IDs are re-assigned so that they run from 1 to the
@ -89,8 +97,8 @@ number of atoms in the system. Note that this is not done for
molecular systems (see the :doc:`atom_style <atom_style>` command),
regardless of the *compress* setting, since it would foul up the bond
connectivity that has already been assigned. However, the
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
accomplish the same thing.
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this
command to accomplish the same thing.
Note that the re-assignment of IDs is not really a compression, where
gaps in atom IDs are removed by decrementing atom IDs that are larger.
@ -100,15 +108,15 @@ the :doc:`create_atoms <create_atoms>` command explains.
A molecular system with fixed bonds, angles, dihedrals, or improper
interactions, is one where the topology of the interactions is
typically defined in the data file read by the
:doc:`read_data <read_data>` command, and where the interactions
themselves are defined with the :doc:`bond_style <bond_style>`,
:doc:`angle_style <angle_style>`, etc commands. If you delete atoms
from such a system, you must be careful not to end up with bonded
interactions that are stored by remaining atoms but which include
deleted atoms. This will cause LAMMPS to generate a "missing atoms"
error when the bonded interaction is computed. The *bond* and *mol*
keywords offer two ways to do that.
typically defined in the data file read by the :doc:`read_data
<read_data>` command, and where the interactions themselves are
defined with the :doc:`bond_style <bond_style>`, :doc:`angle_style
<angle_style>`, etc commands. If you delete atoms from such a system,
you must be careful not to end up with bonded interactions that are
stored by remaining atoms but which include deleted atoms. This will
cause LAMMPS to generate a "missing atoms" error when the bonded
interaction is computed. The *bond* and *mol* keywords offer two ways
to do that.
It the *bond* keyword is set to *yes* then any bond or angle or
dihedral or improper interaction that includes a deleted atom is also

95
doc/src/dump.rst
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@ -137,7 +137,7 @@ Examples
dump myDump all atom/gz 100 dump.atom.gz
dump myDump all atom/zstd 100 dump.atom.zst
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
@ -169,11 +169,12 @@ or multiple smaller files).
.. note::
Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
written to a dump file may be slightly outside the simulation box.
Re-neighbor timesteps will not typically coincide with the timesteps
dump snapshots are written. See the :doc:`dump_modify pbc <dump_modify>` command if you with to force coordinates to be
Because periodic boundary conditions are enforced only on timesteps
when neighbor lists are rebuilt, the coordinates of an atom written
to a dump file may be slightly outside the simulation box.
Re-neighbor timesteps will not typically coincide with the
timesteps dump snapshots are written. See the :doc:`dump_modify
pbc <dump_modify>` command if you with to force coordinates to be
strictly inside the simulation box.
.. note::
@ -189,20 +190,21 @@ or multiple smaller files).
multiple processors, each of which owns a subset of the atoms.
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by
atom ID is on by default. See the :doc:`dump_modify <dump_modify>` doc
page for details.
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
doc page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical
in command syntax to the corresponding styles without "gz", however,
they generate compressed files using the zlib library. Thus the filename
suffix ".gz" is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed network
disallows using the fork() library call (which is needed for a pipe).
For the remainder of this doc page, you should thus consider the *atom*
and *atom/gz* styles (etc) to be inter-changeable, with the exception
of the required filename suffix.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
are identical in command syntax to the corresponding styles without
"gz", however, they generate compressed files using the zlib
library. Thus the filename suffix ".gz" is mandatory. This is an
alternative approach to writing compressed files via a pipe, as done
by the regular dump styles, which may be required on clusters where
the interface to the high-speed network disallows using the fork()
library call (which is needed for a pipe). For the remainder of this
doc page, you should thus consider the *atom* and *atom/gz* styles
(etc) to be inter-changeable, with the exception of the required
filename suffix.
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
@ -219,6 +221,11 @@ you should thus consider the *atom* and *atom/mpiio* styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
The precision of values output to text-based dump files can be
controlled by the :doc:`dump_modify format <dump_modify>` command and
its options.
@ -275,10 +282,11 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic <Howto_triclinic>` page for a geometric description
of triclinic boxes, as defined by LAMMPS, simple formulas for how the
6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from
the triclinic parameters, and how to transform those parameters to and
of xlo, etc, since they represent a bounding box. See the :doc:`Howto
triclinic <Howto_triclinic>` page for a geometric description of
triclinic boxes, as defined by LAMMPS, simple formulas for how the 6
bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the
triclinic parameters, and how to transform those parameters to and
from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
@ -310,23 +318,24 @@ written to the dump file. This local data is typically calculated by
each processor based on the atoms it owns, but there may be zero or
more entities per atom, e.g. a list of bond distances. An explanation
of the possible dump local attributes is given below. Note that by
using input from the :doc:`compute property/local <compute_property_local>` command with dump local,
it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
:doc:`read_data <read_data>` command.
using input from the :doc:`compute property/local
<compute_property_local>` command with dump local, it is possible to
generate information on bonds, angles, etc that can be cut and pasted
directly into a data file read by the :doc:`read_data <read_data>`
command.
Style *cfg* has the same command syntax as style *custom* and writes
extended CFG format files, as used by the
`AtomEye <http://li.mit.edu/Archive/Graphics/A/>`_ visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wildcard "\*" must be included in the filename, as
discussed below. The list of atom attributes for style *cfg* must
begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
since these quantities are needed to write the CFG files in the
appropriate format (though the "mass" and "type" fields do not appear
explicitly in the file). Any remaining attributes will be stored as
"auxiliary properties" in the CFG files. Note that you will typically
want to use the :doc:`dump_modify element <dump_modify>` command with
extended CFG format files, as used by the `AtomEye
<http://li.mit.edu/Archive/Graphics/A/>`_ visualization package.
Since the extended CFG format uses a single snapshot of the system per
file, a wildcard "\*" must be included in the filename, as discussed
below. The list of atom attributes for style *cfg* must begin with
either "mass type xs ys zs" or "mass type xsu ysu zsu" since these
quantities are needed to write the CFG files in the appropriate format
(though the "mass" and "type" fields do not appear explicitly in the
file). Any remaining attributes will be stored as "auxiliary
properties" in the CFG files. Note that you will typically want to
use the :doc:`dump_modify element <dump_modify>` command with
CFG-formatted files, to associate element names with atom types, so
that AtomEye can render atoms appropriately. When unwrapped
coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye
@ -452,6 +461,11 @@ use the :doc:`read_dump <read_dump>` command or perform other
post-processing, just as if the dump file was not written using
MPI-IO.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple
@ -708,8 +722,9 @@ are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
The *xtc* style is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
The *xtc* and *dcd* styles are part of the EXTRA-DUMP package. They
are only enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""

499
doc/src/dump_image.rst
View File

@ -6,6 +6,8 @@ dump image command
dump movie command
==================
(see below for :ref:`dump_modify options <dump_modify_image>` specific to dump image/movie)
Syntax
""""""
@ -15,7 +17,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be imaged
* style = *image* or *movie* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* style = *image* or *movie* = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps
* file = name of file to write image to
* color = atom attribute that determines color of each atom
@ -79,6 +81,69 @@ Syntax
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0
.. _dump_modify_image:
dump_modify options for dump image/movie
========================================
Syntax
""""""
.. parsed-literal::
dump_modify dump-ID keyword values ...
* these keywords apply only to the *image* and *movie* styles and are documented on this page
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
* see the :doc:`dump modify <dump_modify>` doc page for more general keywords
.. parsed-literal::
*acolor* args = type color
type = atom type or range of types (see below)
color = name of color or color1/color2/...
*adiam* args = type diam
type = atom type or range of types (see below)
diam = diameter of atoms of that type (distance units)
*amap* args = lo hi style delta N entry1 entry2 ... entryN
lo = number or *min* = lower bound of range of color map
hi = number or *max* = upper bound of range of color map
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
"c" for continuous
"d" for discrete
"s" for sequential
"a" for absolute
"f" for fractional
delta = binsize (only used for style "s", otherwise ignored)
binsize = range is divided into bins of this width
N = # of subsequent entries
entry = value color (for continuous style)
value = number or *min* or *max* = single value within range
color = name of color used for that value
entry = lo hi color (for discrete style)
lo/hi = number or *min* or *max* = lower/upper bound of subset of range
color = name of color used for that subset of values
entry = color (for sequential style)
color = name of color used for a bin of values
*backcolor* arg = color
color = name of color for background
*bcolor* args = type color
type = bond type or range of types (see below)
color = name of color or color1/color2/...
*bdiam* args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
*boxcolor* arg = color
color = name of color for simulation box lines and processor sub-domain lines
*color* args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
Examples
""""""""
@ -91,6 +156,8 @@ Examples
dump m1 all movie 1000 movie.avi type type size 640 480
dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
Description
"""""""""""
@ -145,10 +212,10 @@ is used.
Similarly, the format of the resulting movie is chosen with the
*movie* dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the `FFmpeg documentation
<http://ffmpeg.org/ffmpeg.html>`_.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the :doc:`dump_modify <dump_modify>` command.
<http://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
compression like bitrate and framerate can be set using the
dump_modify command as described below.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
@ -210,19 +277,20 @@ to colors is as follows:
* type 6 = cyan
and repeats itself for types > 6. This mapping can be changed by the
:doc:`dump_modify acolor <dump_modify>` command.
"dump_modify acolor" command, as described below.
If *type* is specified for the *diameter* setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam <dump_modify>` command.
diameter 1.0. This mapping can be changed by the "dump_modify adiam"
command, as described below.
If *element* is specified for the *color* and/or *diameter* setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the "dump_modify element" command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the `AtomEye <atomeye_>`_ visualization package.
mapping specified by the "dump_modify element" command, as described
below. By default every atom type is C (carbon). Every element has a
color and diameter associated with it, which is the same as the colors
and sizes used by the `AtomEye <atomeye_>`_ visualization package.
.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
@ -232,13 +300,13 @@ settings, they are interpreted in the following way.
If "vx", for example, is used as the *color* setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the
:doc:`dump_modify <dump_modify>` command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange".
a "color map", which can be specified via the dump_modify command, as
described below. The basic idea is that the atom-attribute will be
within a range of values, and every value within the range is mapped
to a specific color. Depending on how the color map is defined, that
mapping can take place via interpolation so that a value of -3.2 is
halfway between "red" and "blue", or discretely so that the value of
-3.2 is "orange".
If "vx", for example, is used as the *diameter* setting, then the atom
will be rendered using the x-component of its velocity as the
@ -251,9 +319,10 @@ diameter, which can be used as the *diameter* setting.
The various keywords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The :doc:`dump modify <dump_modify>`
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
will likely not need to change. As described below, the dump modify
command also has options specific to the dump image style,
particularly for assigning colors to atoms, bonds, and other image
features.
----------
@ -295,7 +364,7 @@ types to colors is as follows:
* type 6 = cyan
and repeats itself for bond types > 6. This mapping can be changed by
the :doc:`dump_modify bcolor <dump_modify>` command.
the "dump_modify bcolor" command, as described below.
The bond *width* value can be a numeric value or *atom* or *type* (or
*none* as indicated above).
@ -310,7 +379,8 @@ of the 2 atoms in the bond.
If *type* is specified for the *width* value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam <dump_modify>` command.
diameter 0.5. This mapping can be changed by the "dump_modify bdiam" command,
as described below.
----------
@ -330,7 +400,7 @@ mapping of types to colors is as follows:
* type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the :doc:`dump_modify <dump_modify>` command.
change this via the dump_modify command.
The line *width* can only be a numeric value, which specifies that all
lines will be drawn as cylinders with that diameter, e.g. 1.0, which
@ -357,7 +427,7 @@ default the mapping of types to colors is as follows:
* type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the :doc:`dump_modify <dump_modify>` command.
change this via the dump_modify command.
----------
@ -390,7 +460,7 @@ particle. By default the mapping of types to colors is as follows:
* type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the :doc:`dump_modify <dump_modify>` command.
change this via the dump_modify command.
----------
@ -414,7 +484,7 @@ the mapping of types to colors is as follows:
* type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the :doc:`dump_modify <dump_modify>` command.
change this via the dump_modify command.
----------
@ -488,7 +558,8 @@ are rendered as thin cylinders in the image. If *no* is set, then the
box boundaries are not drawn and the *diam* setting is ignored. If
*yes* is set, the 12 edges of the box are drawn, with a diameter that
is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
2d). The color of the box boundaries can be set with the "dump_modify
boxcolor" command.
The *axes* keyword determines if and how the coordinate axes are
rendered as thin cylinders in the image. If *no* is set, then the
@ -507,7 +578,8 @@ set (default), then the sub-domain boundaries are not drawn and the
*diam* setting is ignored. If *yes* is set, the 12 edges of each
processor sub-domain are drawn, with a diameter that is a fraction of
the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
of the sub-domain boundaries can be set with the "dump_modify
boxcolor" command.
----------
@ -607,9 +679,272 @@ Play the movie:
----------
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities
which could then be output into dump files.
Dump_modify keywords for dump image and dump movie
""""""""""""""""""""""""""""""""""""""""""""""""""
The following dump_modify keywords apply only to the dump image and
dump movie styles. Any keyword that works with dump image also works
with dump movie, since the movie is simply a collection of images.
Some of the keywords only affect the dump movie style. The
descriptions give details.
----------
The *acolor* keyword can be used with the dump image command, when its
atom color setting is *type*, to set the color that atoms of each type
will be drawn in the image.
The specified *type* should be an integer from 1 to Ntypes = the
number of atom types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of atom types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the
"dump_modify color" command, as described below. Or it can be two or
more colors separated by a "/" character, e.g. red/green/blue. In the
former case, that color is assigned to all the specified atom types.
In the latter case, the list of colors are assigned in a round-robin
fashion to each of the specified atom types.
----------
The *adiam* keyword can be used with the dump image command, when its
atom diameter setting is *type*, to set the size that atoms of each
type will be drawn in the image. The specified *type* should be an
integer from 1 to Ntypes. As with the *acolor* keyword, a wildcard
asterisk can be used as part of the *type* argument to specify a range
of atom types. The specified *diam* is the size in whatever distance
:doc:`units <units>` the input script is using, e.g. Angstroms.
----------
The *amap* keyword can be used with the dump image command, with its
*atom* keyword, when its atom setting is an atom-attribute, to setup a
color map. The color map is used to assign a specific RGB
(red/green/blue) color value to an individual atom when it is drawn,
based on the atom's attribute, which is a numeric value, e.g. its
x-component of velocity if the atom-attribute "vx" was specified.
The basic idea of a color map is that the atom-attribute will be
within a range of values, and that range is associated with a series
of colors (e.g. red, blue, green). An atom's specific value (vx =
-3.2) can then mapped to the series of colors (e.g. halfway between
red and blue), and a specific color is determined via an interpolation
procedure.
There are many possible options for the color map, enabled by the
*amap* keyword. Here are the details.
The *lo* and *hi* settings determine the range of values allowed for
the atom attribute. If numeric values are used for *lo* and/or *hi*,
then values that are lower/higher than that value are set to the
value. I.e. the range is static. If *lo* is specified as *min* or
*hi* as *max* then the range is dynamic, and the lower and/or
upper bound will be calculated each time an image is drawn, based
on the set of atoms being visualized.
The *style* setting is two letters, such as "ca". The first letter is
either "c" for continuous, "d" for discrete, or "s" for sequential.
The second letter is either "a" for absolute, or "f" for fractional.
A continuous color map is one in which the color changes continuously
from value to value within the range. A discrete color map is one in
which discrete colors are assigned to sub-ranges of values within the
range. A sequential color map is one in which discrete colors are
assigned to a sequence of sub-ranges of values covering the entire
range.
An absolute color map is one in which the values to which colors are
assigned are specified explicitly as values within the range. A
fractional color map is one in which the values to which colors are
assigned are specified as a fractional portion of the range. For
example if the range is from -10.0 to 10.0, and the color red is to be
assigned to atoms with a value of 5.0, then for an absolute color map
the number 5.0 would be used. But for a fractional map, the number
0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
The *delta* setting must be specified for all styles, but is only used
for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
the range. The first will be from -10.0 <= color1 < -9.0, then second
from -9.0 <= color2 < -8.0, etc.
The *N* setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or
sequential. In all cases the *color* setting can be any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option.
For continuous color maps, each entry has a *value* and a *color*\ .
The *value* is either a number within the range of values or *min* or
*max*\ . The *value* of the first entry must be *min* and the *value*
of the last entry must be *max*\ . Any entries in between must have
increasing values. Note that numeric values can be specified either
as absolute numbers or as fractions (0.0 to 1.0) of the range,
depending on the "a" or "f" in the style setting for the color map.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. X will fall
between 2 of the entry values. The color of the atom is linearly
interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if X = -5.0 and the 2
surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
atom's color will be halfway between "red" and "blue", which happens
to be "purple".
For discrete color maps, each entry has a *lo* and *hi* value and a
*color*\ . The *lo* and *hi* settings are either numbers within the
range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
and *hi* settings of the last entry must be *min* and *max*\ . Other
entries can have any *lo* and *hi* values and the sub-ranges of
different values can overlap. Note that numeric *lo* and *hi* values
can be specified either as absolute numbers or as fractions (0.0 to
1.0) of the range, depending on the "a" or "f" in the style setting
for the color map.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. The entries
are scanned from first to last. The first time that *lo* <= X <=
*hi*, X is assigned the color associated with that entry. You can
think of the last entry as assigning a default color (since it will
always be matched by X), and the earlier entries as colors that
override the default. Also note that no interpolation of a color RGB
is done. All atoms will be drawn with one of the colors in the list
of entries.
For sequential color maps, each entry has only a *color*\ . Here is how
the entries are used to determine the color of an individual atom,
given the value X of its atom attribute. The range is partitioned
into N bins of width *binsize*\ . Thus X will fall in a specific bin
from 1 to N, say the Mth bin. If it falls on a boundary between 2
bins, it is considered to be in the higher of the 2 bins. Each bin is
assigned a color from the E entries. If E < N, then the colors are
repeated. For example if 2 entries with colors red and green are
specified, then the odd numbered bins will be red and the even bins
green. The color of the atom is the color of its bin. Note that the
sequential color map is really a shorthand way of defining a discrete
color map without having to specify where all the bin boundaries are.
Here is an example of using a sequential color map to color all the
atoms in individual molecules with a different color. See the
examples/pour/in.pour.2d.molecule input script for an example of how
this is used.
.. code-block:: LAMMPS
variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
In this case, 10 colors are defined, and molecule IDs are
mapped to one of the colors, even if there are 1000s of molecules.
----------
The *backcolor* sets the background color of the images. The color
name can be any of the 140 pre-defined colors (see below) or a color
name defined by the dump_modify color option.
----------
The *bcolor* keyword can be used with the dump image command, with its
*bond* keyword, when its color setting is *type*, to set the color
that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Nbondtypes = the
number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option. Or it can be two or more colors separated
by a "/" character, e.g. red/green/blue. In the former case, that
color is assigned to all the specified bond types. In the latter
case, the list of colors are assigned in a round-robin fashion to each
of the specified bond types.
----------
The *bdiam* keyword can be used with the dump image command, with its
*bond* keyword, when its diam setting is *type*, to set the diameter
that bonds of each type will be drawn in the image. The specified
*type* should be an integer from 1 to Nbondtypes. As with the
*bcolor* keyword, a wildcard asterisk can be used as part of the
*type* argument to specify a range of bond types. The specified
*diam* is the size in whatever distance :doc:`units <units>` you are
using, e.g. Angstroms.
----------
The *bitrate* keyword can be used with the :doc:`dump movie
<dump_image>` command to define the size of the resulting movie file
and its quality via setting how many kbits per second are to be used
for the movie file. Higher bitrates require less compression and will
result in higher quality movies. The quality is also determined by
the compression format and encoder. The default setting is 2000
kbit/s, which will result in average quality with older compression
formats.
.. note::
Not all movie file formats supported by dump movie allow the
bitrate to be set. If not, the setting is silently ignored.
----------
The *boxcolor* keyword sets the color of the simulation box drawn
around the atoms in each image as well as the color of processor
sub-domain boundaries. See the "dump image box" command for how to
specify that a box be drawn via the *box* keyword, and the sub-domain
boundaries via the *subbox* keyword. The color name can be any of the
140 pre-defined colors (see below) or a color name defined by the
dump_modify color option.
----------
The *color* keyword allows definition of a new color name, in addition
to the 140-predefined colors (see below), and associates 3
red/green/blue RGB values with that color name. The color name can
then be used with any other dump_modify keyword that takes a color
name as a value. The RGB values should each be floating point values
between 0.0 and 1.0 inclusive.
When a color name is converted to RGB values, the user-defined color
names are searched first, then the 140 pre-defined color names. This
means you can also use the *color* keyword to overwrite one of the
pre-defined color names with new RBG values.
----------
The *framerate* keyword can be used with the :doc:`dump movie
<dump_image>` command to define the duration of the resulting movie
file. Movie files written by the dump *movie* command have a default
frame rate of 24 frames per second and the images generated will be
converted at that rate. Thus a sequence of 1000 dump images will
result in a movie of about 42 seconds. To make a movie run longer you
can either generate images more frequently or lower the frame rate.
To speed a movie up, you can do the inverse. Using a frame rate
higher than 24 is not recommended, as it will result in simply
dropping the rendered images. It is more efficient to dump images less
frequently.
----------
@ -664,7 +999,7 @@ Related commands
Default
"""""""
The defaults for the keywords are as follows:
The defaults for the dump image and dump movie keywords are as follows:
* adiam = not specified (use diameter setting)
* atom = yes
@ -682,3 +1017,101 @@ The defaults for the keywords are as follows:
* subbox no 0.0
* shiny = 1.0
* ssao = no
----------
The defaults for the dump_modify keywords specific to dump image and dump movie are as follows:
* acolor = \* red/green/blue/yellow/aqua/cyan
* adiam = \* 1.0
* amap = min max cf 0.0 2 min blue max red
* backcolor = black
* bcolor = \* red/green/blue/yellow/aqua/cyan
* bdiam = \* 0.5
* bitrate = 2000
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
----------
These are the standard 109 element names that LAMMPS pre-defines for
use with the dump image and dump_modify commands.
* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
----------
These are the 140 colors that LAMMPS pre-defines for use with the dump
image and dump_modify commands. Additional colors can be defined with
the dump_modify color command. The 3 numbers listed for each name are
the RGB (red/green/blue) values. Divide each value by 255 to get the
equivalent 0.0 to 1.0 value.
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+

613
doc/src/dump_modify.rst
View File

@ -3,6 +3,9 @@
dump_modify command
===================
:doc:`dump_modify <dump_image>` command for image/movie options
===============================================================
Syntax
""""""
@ -12,8 +15,9 @@ Syntax
* dump-ID = ID of dump to modify
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
.. parsed-literal::
@ -28,6 +32,9 @@ Syntax
*every* arg = N
N = dump every this many timesteps
N can be a variable (see below)
*every/time* arg = Delta
Delta = dump every this interval in simulation time (time units)
Delta can be a variable (see below)
*fileper* arg = Np
Np = write one file for every this many processors
*first* arg = *yes* or *no*
@ -35,6 +42,9 @@ Syntax
*format* args = *line* string, *int* string, *float* string, M string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of per-atom quantities being output
*header* arg = *yes* or *no*
*yes* to write the header
*no* to not write the header
*image* arg = *yes* or *no*
*label* arg = string
string = character string (e.g. BONDS) to use in header of dump local file
@ -66,56 +76,11 @@ Syntax
*unwrap* arg = *yes* or *no*
* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
.. parsed-literal::
*acolor* args = type color
type = atom type or range of types (see below)
color = name of color or color1/color2/...
*adiam* args = type diam
type = atom type or range of types (see below)
diam = diameter of atoms of that type (distance units)
*amap* args = lo hi style delta N entry1 entry2 ... entryN
lo = number or *min* = lower bound of range of color map
hi = number or *max* = upper bound of range of color map
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
"c" for continuous
"d" for discrete
"s" for sequential
"a" for absolute
"f" for fractional
delta = binsize (only used for style "s", otherwise ignored)
binsize = range is divided into bins of this width
N = # of subsequent entries
entry = value color (for continuous style)
value = number or *min* or *max* = single value within range
color = name of color used for that value
entry = lo hi color (for discrete style)
lo/hi = number or *min* or *max* = lower/upper bound of subset of range
color = name of color used for that subset of values
entry = color (for sequential style)
color = name of color used for a bin of values
*backcolor* arg = color
color = name of color for background
*bcolor* args = type color
type = bond type or range of types (see below)
color = name of color or color1/color2/...
*bdiam* args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
*boxcolor* arg = color
color = name of color for simulation box lines and processor sub-domain lines
*color* args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
*header* arg = *yes* or *no*
*yes* to write the header
*no* to not write the header
see the :doc:`dump image <dump_image>` doc page for details
* these keywords apply only to the */gz* and */zstd* dump styles
* keyword = *compression_level*
@ -126,7 +91,7 @@ Syntax
level = integer specifying the compression level that should be used (see below for supported levels)
* these keywords apply only to the */zstd* dump styles
* keyword = *compression_level*
* keyword = *checksum*
.. parsed-literal::
@ -144,7 +109,6 @@ Examples
dump_modify xtcdump precision 10000 sfactor 0.1
dump_modify 1 every 1000 nfile 20
dump_modify 1 every v_myVar
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
Description
"""""""""""
@ -163,8 +127,9 @@ which allow for use of MPI-IO.
----------
These keywords apply to various dump styles, including the :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles. The
description gives details.
Unless otherwise noted, the following keywords apply to all the
various dump styles, including the :doc:`dump image <dump_image>` and
:doc:`dump movie <dump_image>` styles.
----------
@ -235,11 +200,19 @@ will be accepted.
----------
The *every* keyword changes the dump frequency originally specified by
the :doc:`dump <dump>` command to a new value. The every keyword can be
specified in one of two ways. It can be a numeric value in which case
it must be > 0. Or it can be an :doc:`equal-style variable <variable>`,
which should be specified as v_name, where name is the variable name.
The *every* keyword can be used with any dump style except the *dcd*
and *xtc* styles. It does two things. It specifies that the interval
between dump snapshots will be set in timesteps, which is the default
if the *every* or *every/time* keywords are not used. See the
*every/time* keyword for how to specify the interval in simulation
time, i.e. in time units of the :doc:`units <units>` command. The
*every* keyword also sets the interval value, which overrides the dump
frequency originally specified by the :doc:`dump <dump>` command.
The *every* keyword can be specified in one of two ways. It can be a
numeric value in which case it must be > 0. Or it can be an
:doc:`equal-style variable <variable>`, which should be specified as
v_name, where name is the variable name.
In this case, the variable is evaluated at the beginning of a run to
determine the next timestep at which a dump snapshot will be written
@ -248,11 +221,12 @@ determine the next timestep, etc. Thus the variable should return
timestep values. See the stagger() and logfreq() and stride() math
functions for :doc:`equal-style variables <variable>`, as examples of
useful functions to use in this context. Other similar math functions
could easily be added as options for :doc:`equal-style variables <variable>`. Also see the next() function, which allows
use of a file-style variable which reads successive values from a
file, each time the variable is evaluated. Used with the *every*
keyword, if the file contains a list of ascending timesteps, you can
output snapshots whenever you wish.
could easily be added as options for :doc:`equal-style variables
<variable>`. Also see the next() function, which allows use of a
file-style variable which reads successive values from a file, each
time the variable is evaluated. Used with the *every* keyword, if the
file contains a list of ascending timesteps, you can output snapshots
whenever you wish.
Note that when using the variable option with the *every* keyword, you
need to use the *first* option if you want an initial snapshot written
@ -293,14 +267,103 @@ in file tmp.times:
----------
The *every/time* keyword can be used with any dump style except the
*dcd* and *xtc* styles. It does two things. It specifies that the
interval between dump snapshots will be set in simulation time,
i.e. in time units of the :doc:`units <units>` command. This can be
useful when the timestep size varies during a simulation run, e.g. by
use of the :doc:`fix dt/reset <fix_dt_reset>` command. The default is
to specify the interval in timesteps; see the *every* keyword. The
*every/time* command also sets the interval value.
.. note::
If you wish dump styles *atom*, *custom*, *local*, or *xyz* to
include the simulation time as a field in the header portion of
each snapshot, you also need to use the dump_modify *time* keyword
with a setting of *yes*. See its documentation below.
Note that since snapshots are output on simulation steps, each
snapshot will be written on the first timestep whose associated
simulation time is >= the exact snapshot time value.
As with the *every* option, the *Delta* value can be specified in one
of two ways. It can be a numeric value in which case it must be >
0.0. Or it can be an :doc:`equal-style variable <variable>`, which
should be specified as v_name, where name is the variable name.
In this case, the variable is evaluated at the beginning of a run to
determine the next simulation time at which a dump snapshot will be
written out. On that timestep the variable will be evaluated again to
determine the next simulation time, etc. Thus the variable should
return values in time units. Note the current timestep or simulation
time can be used in an :doc:`equal-style variables <variable>` since
they are both thermodynamic keywords. Also see the next() function,
which allows use of a file-style variable which reads successive
values from a file, each time the variable is evaluated. Used with
the *every/time* keyword, if the file contains a list of ascending
simulation times, you can output snapshots whenever you wish.
Note that when using the variable option with the *every/time*
keyword, you need to use the *first* option if you want an initial
snapshot written to the dump file. The *every/time* keyword cannot be
used with the dump *dcd* style.
For example, the following commands will write snapshots at successive
simulation times which grow by a factor of 1.5 with each interval.
The dt value used in the variable is to avoid a zero result when the
initial simulation time is 0.0.
.. code-block:: LAMMPS
variable increase equal 1.5*(time+dt)
dump 1 all atom 100 tmp.dump
dump_modify 1 every/time v_increase first yes
The following commands would write snapshots at the times listed in
file tmp.times:
.. code-block:: LAMMPS
variable f file tmp.times
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every/time v_s
.. note::
When using a file-style variable with the *every/time* keyword, the
file of timesteps must list a first time that is beyond the time
associated with the current timestep (e.g. it cannot be 0.0). And
it must list one or more times beyond the length of the run you
perform. This is because the dump command will generate an error
if the next time it reads from the file is not a value greater than
the current time. Thus if you wanted output at times 0,15,100 of a
run of length 100 in simulation time, the file should contain the
values 15,100,101 and you should also use the dump_modify first
command. Any final value > 100 could be used in place of 101.
----------
The *first* keyword determines whether a dump snapshot is written on
the very first timestep after the dump command is invoked. This will
always occur if the current timestep is a multiple of N, the frequency
specified in the :doc:`dump <dump>` command, including timestep 0. But
if this is not the case, a dump snapshot will only be written if the
setting of this keyword is *yes*\ . If it is *no*, which is the
always occur if the current timestep is a multiple of $N$, the
frequency specified in the :doc:`dump <dump>` command or
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
It will also always occur if the current simulation time is a multiple
of *Delta*, the time interval specified in the doc:`dump_modify
every/time <dump_modify>` command.
But if this is not the case, a dump snapshot will only be written if
the setting of this keyword is *yes*\ . If it is *no*, which is the
default, then it will not be written.
Note that if the argument to the :doc:`dump_modify every
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
a variable and not a numeric value, then specifying *first yes* is the
only way to write a dump snapshot on the first timestep after the dump
command is invoked.
----------
The *flush* keyword determines whether a flush operation is invoked
@ -380,6 +443,13 @@ The *fileper* keyword is documented below with the *nfile* keyword.
----------
The *header* keyword toggles whether the dump file will include a
header. Excluding a header will reduce the size of the dump file for
fixes such as :doc:`fix pair/tracker <fix_pair_tracker>` which do not
require the information typically written to the header.
----------
The *image* keyword applies only to the dump *atom* style. If the
image value is *yes*, 3 flags are appended to each atom's coords which
are the absolute box image of the atom in each dimension. For
@ -592,7 +662,9 @@ The dump *local* style cannot be sorted by atom ID, since there are
typically multiple lines of output per atom. Some dump styles, such
as *dcd* and *xtc*, require sorting by atom ID to format the output
file correctly. If multiple processors are writing the dump file, via
the "%" wildcard in the dump filename, then sorting cannot be
the "%" wildcard in the dump filename and the *nfile* or *fileper*
keywords are set to non-default values (i.e. the number of dump file
pieces is not equal to the number of procs), then sorting cannot be
performed.
.. note::
@ -670,16 +742,20 @@ threshold criterion is met. Otherwise it is not met.
----------
The *time* keyword only applies to the dump *atom*, *custom*, and
*local* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). If set to *yes*, each frame will will
contain two extra lines before the "ITEM: TIMESTEP" entry:
The *time* keyword only applies to the dump *atom*, *custom*, *local*,
and *xyz* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). For the first 3 styles, if set to
*yes*, each frame will will contain two extra lines before the "ITEM:
TIMESTEP" entry:
.. parsed-literal::
ITEM: TIME
\<elapsed time\>
For the *xyz* style, the simulation time is included on the same line
as the timestep value.
This will output the current elapsed simulation time in current
time units equivalent to the :doc:`thermo keyword <thermo_style>` *time*\ .
This is to simplify post-processing of trajectories using a variable time
@ -715,303 +791,35 @@ box size stored with the snapshot.
----------
These keywords apply only to the :doc:`dump image <dump_image>` and
:doc:`dump movie <dump_image>` styles. Any keyword that affects an
image, also affects a movie, since the movie is simply a collection of
images. Some of the keywords only affect the :doc:`dump movie <dump_image>` style. The descriptions give details.
The COMPRESS package offers both GZ and Zstd compression variants of
styles atom, custom, local, cfg, and xyz. When using these styles the
compression level can be controlled by the :code:`compression_level`
keyword. File names with these styles have to end in either
:code:`.gz` or :code:`.zst`.
----------
The *acolor* keyword can be used with the :doc:`dump image <dump_image>`
command, when its atom color setting is *type*, to set the color that
atoms of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Ntypes = the
number of atom types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option. Or it can be two or more colors separated
by a "/" character, e.g. red/green/blue. In the former case, that
color is assigned to all the specified atom types. In the latter
case, the list of colors are assigned in a round-robin fashion to each
of the specified atom types.
----------
The *adiam* keyword can be used with the :doc:`dump image <dump_image>`
command, when its atom diameter setting is *type*, to set the size
that atoms of each type will be drawn in the image. The specified
*type* should be an integer from 1 to Ntypes. As with the *acolor*
keyword, a wildcard asterisk can be used as part of the *type*
argument to specify a range of atom types. The specified *diam* is
the size in whatever distance :doc:`units <units>` the input script is
using, e.g. Angstroms.
----------
The *amap* keyword can be used with the :doc:`dump image <dump_image>`
command, with its *atom* keyword, when its atom setting is an
atom-attribute, to setup a color map. The color map is used to assign
a specific RGB (red/green/blue) color value to an individual atom when
it is drawn, based on the atom's attribute, which is a numeric value,
e.g. its x-component of velocity if the atom-attribute "vx" was
specified.
The basic idea of a color map is that the atom-attribute will be
within a range of values, and that range is associated with a series
of colors (e.g. red, blue, green). An atom's specific value (vx =
-3.2) can then mapped to the series of colors (e.g. halfway between
red and blue), and a specific color is determined via an interpolation
procedure.
There are many possible options for the color map, enabled by the
*amap* keyword. Here are the details.
The *lo* and *hi* settings determine the range of values allowed for
the atom attribute. If numeric values are used for *lo* and/or *hi*,
then values that are lower/higher than that value are set to the
value. I.e. the range is static. If *lo* is specified as *min* or
*hi* as *max* then the range is dynamic, and the lower and/or
upper bound will be calculated each time an image is drawn, based
on the set of atoms being visualized.
The *style* setting is two letters, such as "ca". The first letter is
either "c" for continuous, "d" for discrete, or "s" for sequential.
The second letter is either "a" for absolute, or "f" for fractional.
A continuous color map is one in which the color changes continuously
from value to value within the range. A discrete color map is one in
which discrete colors are assigned to sub-ranges of values within the
range. A sequential color map is one in which discrete colors are
assigned to a sequence of sub-ranges of values covering the entire
range.
An absolute color map is one in which the values to which colors are
assigned are specified explicitly as values within the range. A
fractional color map is one in which the values to which colors are
assigned are specified as a fractional portion of the range. For
example if the range is from -10.0 to 10.0, and the color red is to be
assigned to atoms with a value of 5.0, then for an absolute color map
the number 5.0 would be used. But for a fractional map, the number
0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
The *delta* setting must be specified for all styles, but is only used
for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
the range. The first will be from -10.0 <= color1 < -9.0, then second
from -9.0 <= color2 < -8.0, etc.
The *N* setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or
sequential. In all cases the *color* setting can be any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option.
For continuous color maps, each entry has a *value* and a *color*\ .
The *value* is either a number within the range of values or *min* or
*max*\ . The *value* of the first entry must be *min* and the *value*
of the last entry must be *max*\ . Any entries in between must have
increasing values. Note that numeric values can be specified either
as absolute numbers or as fractions (0.0 to 1.0) of the range,
depending on the "a" or "f" in the style setting for the color map.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. X will fall
between 2 of the entry values. The color of the atom is linearly
interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if X = -5.0 and the 2
surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
atom's color will be halfway between "red" and "blue", which happens
to be "purple".
For discrete color maps, each entry has a *lo* and *hi* value and a
*color*\ . The *lo* and *hi* settings are either numbers within the
range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
and *hi* settings of the last entry must be *min* and *max*\ . Other
entries can have any *lo* and *hi* values and the sub-ranges of
different values can overlap. Note that numeric *lo* and *hi* values
can be specified either as absolute numbers or as fractions (0.0 to
1.0) of the range, depending on the "a" or "f" in the style setting
for the color map.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. The entries
are scanned from first to last. The first time that *lo* <= X <=
*hi*, X is assigned the color associated with that entry. You can
think of the last entry as assigning a default color (since it will
always be matched by X), and the earlier entries as colors that
override the default. Also note that no interpolation of a color RGB
is done. All atoms will be drawn with one of the colors in the list
of entries.
For sequential color maps, each entry has only a *color*\ . Here is how
the entries are used to determine the color of an individual atom,
given the value X of its atom attribute. The range is partitioned
into N bins of width *binsize*\ . Thus X will fall in a specific bin
from 1 to N, say the Mth bin. If it falls on a boundary between 2
bins, it is considered to be in the higher of the 2 bins. Each bin is
assigned a color from the E entries. If E < N, then the colors are
repeated. For example if 2 entries with colors red and green are
specified, then the odd numbered bins will be red and the even bins
green. The color of the atom is the color of its bin. Note that the
sequential color map is really a shorthand way of defining a discrete
color map without having to specify where all the bin boundaries are.
Here is an example of using a sequential color map to color all the
atoms in individual molecules with a different color. See the
examples/pour/in.pour.2d.molecule input script for an example of how
this is used.
.. code-block:: LAMMPS
variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
In this case, 10 colors are defined, and molecule IDs are
mapped to one of the colors, even if there are 1000s of molecules.
----------
The *backcolor* sets the background color of the images. The color
name can be any of the 140 pre-defined colors (see below) or a color
name defined by the dump_modify color option.
----------
The *bcolor* keyword can be used with the :doc:`dump image <dump_image>`
command, with its *bond* keyword, when its color setting is *type*, to
set the color that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Nbondtypes = the
number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of bond types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option. Or it can be two or more colors separated
by a "/" character, e.g. red/green/blue. In the former case, that
color is assigned to all the specified bond types. In the latter
case, the list of colors are assigned in a round-robin fashion to each
of the specified bond types.
----------
The *bdiam* keyword can be used with the :doc:`dump image <dump_image>`
command, with its *bond* keyword, when its diam setting is *type*, to
set the diameter that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Nbondtypes. As
with the *bcolor* keyword, a wildcard asterisk can be used as part of
the *type* argument to specify a range of bond types. The specified
*diam* is the size in whatever distance :doc:`units <units>` you are
using, e.g. Angstroms.
----------
The *bitrate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the size of the resulting
movie file and its quality via setting how many kbits per second are
to be used for the movie file. Higher bitrates require less
compression and will result in higher quality movies. The quality is
also determined by the compression format and encoder. The default
setting is 2000 kbit/s, which will result in average quality with
older compression formats.
.. note::
Not all movie file formats supported by dump movie allow the
bitrate to be set. If not, the setting is silently ignored.
----------
The *boxcolor* keyword sets the color of the simulation box drawn
around the atoms in each image as well as the color of processor
sub-domain boundaries. See the "dump image box" command for how to
specify that a box be drawn via the *box* keyword, and the sub-domain
boundaries via the *subbox* keyword. The color name can be any of the
140 pre-defined colors (see below) or a color name defined by the
dump_modify color option.
----------
The *color* keyword allows definition of a new color name, in addition
to the 140-predefined colors (see below), and associates 3
red/green/blue RGB values with that color name. The color name can
then be used with any other dump_modify keyword that takes a color
name as a value. The RGB values should each be floating point values
between 0.0 and 1.0 inclusive.
When a color name is converted to RGB values, the user-defined color
names are searched first, then the 140 pre-defined color names. This
means you can also use the *color* keyword to overwrite one of the
pre-defined color names with new RBG values.
----------
The *framerate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the duration of the resulting
movie file. Movie files written by the dump *movie* command have a
default frame rate of 24 frames per second and the images generated
will be converted at that rate. Thus a sequence of 1000 dump images
will result in a movie of about 42 seconds. To make a movie run
longer you can either generate images more frequently or lower the
frame rate. To speed a movie up, you can do the inverse. Using a
frame rate higher than 24 is not recommended, as it will result in
simply dropping the rendered images. It is more efficient to dump
images less frequently.
----------
The *header* keyword toggles whether the dump file will include a header.
Excluding a header will reduce the size of the dump file for fixes such as
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
typically written to the header.
----------
The COMPRESS package offers both GZ and Zstd compression variants of styles
atom, custom, local, cfg, and xyz. When using these styles the compression
level can be controlled by the :code:`compression_level` parameter. File names
with these styles have to end in either :code:`.gz` or :code:`.zst`.
GZ supports compression levels from -1 (default), 0 (no compression), and 1 to
9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9 as
default compression level.
GZ supports compression levels from -1 (default), 0 (no compression),
and 1 to
9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9
as default compression level.
Zstd offers a wider range of compression levels, including negative
levels that sacrifice compression for performance. 0 is the
default, positive levels are 1 to 22, with 22 being the most expensive
levels that sacrifice compression for performance. 0 is the default,
positive levels are 1 to 22, with 22 being the most expensive
compression. Zstd promises higher compression/decompression speeds for
similar compression ratios. For more details see
`http://facebook.github.io/zstd/`.
In addition, Zstd compressed files can have a checksum of the entire
contents. The Zstd enabled dump styles enable this feature by default and it
can be disabled with the :code:`checksum` parameter.
In addition, Zstd compressed files can include a checksum of the
entire contents. The Zstd enabled dump styles enable this feature by
default and it can be disabled with the :code:`checksum` keyword.
----------
Restrictions
""""""""""""
none
Not all *dump_modify* options can be applied to all dump styles.
Details are in the discussions of the individual options.
Related commands
""""""""""""""""
@ -1046,100 +854,7 @@ The option defaults are
* units = no
* unwrap = no
* acolor = \* red/green/blue/yellow/aqua/cyan
* adiam = \* 1.0
* amap = min max cf 0.0 2 min blue max red
* backcolor = black
* bcolor = \* red/green/blue/yellow/aqua/cyan
* bdiam = \* 0.5
* bitrate = 2000
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
* compression_level = 9 (gz variants)
* compression_level = 0 (zstd variants)
* checksum = yes (zstd variants)
----------
These are the standard 109 element names that LAMMPS pre-defines for
use with the :doc:`dump image <dump_image>` and dump_modify commands.
* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
----------
These are the 140 colors that LAMMPS pre-defines for use with the
:doc:`dump image <dump_image>` and dump_modify commands. Additional
colors can be defined with the dump_modify color command. The 3
numbers listed for each name are the RGB (red/green/blue) values.
Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 |
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+

2
doc/src/fix_addtorque.rst
View File

@ -99,7 +99,7 @@ invoked by the :doc:`minimize <minimize>` command.
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.

18
doc/src/fix_dt_reset.rst
View File

@ -78,13 +78,20 @@ outer loop (largest) timestep, which is the same timestep that the
Note that the cumulative simulation time (in time units), which
accounts for changes in the timestep size as a simulation proceeds,
can be accessed by the :doc:`thermo_style time <thermo_style>` keyword.
can be accessed by the :doc:`thermo_style time <thermo_style>`
keyword.
Also note that the :doc:`dump_modify every/time <dump_modify>` option
allows dump files to be written at intervals specified by simulation
time, rather than by timesteps. Simulation time is in time units;
see the :doc:`units <units>` doc page for details.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar stores the last
@ -93,7 +100,8 @@ timestep on which the timestep was reset to a new value.
The scalar value calculated by this fix is "intensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -102,7 +110,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`timestep <timestep>`
:doc:`timestep <timestep>`, :doc:`dump_modify every/time <dump_modify>`
Default
"""""""

4
doc/src/fix_langevin_drude.rst
View File

@ -40,7 +40,7 @@ Example input scripts available: examples/PACKAGES/drude
Description
"""""""""""
Apply two Langevin thermostats as described in :ref:`(Jiang) <Jiang1>` for
Apply two Langevin thermostats as described in :ref:`(Jiang1) <Jiang1>` for
thermalizing the reduced degrees of freedom of Drude oscillators.
This link describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>` in LAMMPS and polarizable models in LAMMPS
are discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc
@ -300,5 +300,5 @@ The option defaults are zero = no.
.. _Jiang1:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
**(Jiang1)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
Phys Chem Lett, 2, 87-92 (2011).

2
doc/src/fix_oneway.rst
View File

@ -51,7 +51,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if LAMMPS
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands

2
doc/src/fix_smd.rst
View File

@ -144,7 +144,7 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands

2
doc/src/kspace_style.rst
View File

@ -310,7 +310,7 @@ Forschungszentrum Juelich.
The library is available for download at "http://scafacos.de" or can
be cloned from the git-repository
"git://github.com/scafacos/scafacos.git".
"https://github.com/scafacos/scafacos.git".
In order to use this KSpace style, you must download and build the
ScaFaCoS library, then build LAMMPS with the SCAFACOS package

2
doc/src/pair_granular.rst
View File

@ -205,7 +205,7 @@ For *damping mass_velocity*, the normal damping is given by:
\eta_n = \eta_{n0} m_{eff}
Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
contact model, in units of *mass*\ /\ *time* and
contact model, in units of 1/\ *time* and
:math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass.
Use *damping mass_velocity* to reproduce the damping behavior of
*pair gran/hooke/\**.

44
doc/src/pair_hybrid.rst
View File

@ -74,14 +74,17 @@ atoms interact with each other via an *eam* potential, the surface atoms
interact with each other via a *lj/cut* potential, and the metal/surface
interaction is also computed via a *lj/cut* potential. The
*hybrid/overlay* style could be used as in the second example above,
where multiple potentials are superposed in an additive fashion to
where multiple potentials are superimposed in an additive fashion to
compute the interaction between atoms. In this example, using *lj/cut*
and *coul/long* together gives the same result as if the
*lj/cut/coul/long* potential were used by itself. In this case, it
would be more efficient to use the single combined potential, but in
general any combination of pair potentials can be used together in to
produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.
file, e.g. adding Coulombic forces between granular particles. Another
limitation of using the *hybrid/overlay* variant, that it does not generate
*lj/cut* parameters for mixed atom types from a mixing rule due to
restrictions discussed below.
If the *hybrid/scaled* style is used instead of *hybrid/overlay*,
contributions from sub-styles are weighted by their scale factors, which
@ -150,10 +153,14 @@ with Tersoff, and the cross-interactions with Lennard-Jones:
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5
If pair coefficients are specified in the data file read via the
:doc:`read_data <read_data>` command, then the same rule applies.
E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for
each line in the "Pair Coeffs" section, e.g.
It is not recommended to read pair coefficients for a hybrid style from a "Pair Coeffs"
or "PairIJ Coeffs" section of a data file via the :doc:`read_data <read_data>` command,
since those sections expect a fixed number of lines, either one line per atom type or
one line pair pair of atom types, respectively. When reading from a data file, the
lines of the "Pair Coeffs" and "PairIJ Coeffs" are changed in the same way as the *pair_coeff*
command, i.e. the name of the pair style to which the parameters apply must follow the
atom type (or atom types), e.g.
.. parsed-literal::
@ -162,6 +169,11 @@ each line in the "Pair Coeffs" section, e.g.
1 lj/cut/coul/cut 1.0 1.0
...
PairIJ Coeffs
1 1 lj/cut/coul/cut 1.0 1.0
...
Note that the pair_coeff command for some potentials such as
:doc:`pair_style eam/alloy <pair_eam>` includes a mapping specification
of elements to all atom types, which in the hybrid case, can include
@ -208,12 +220,22 @@ examples above, or in the data file read by the :doc:`read_data
<read_data>`, or by mixing as described below. Also all sub-styles
must be used at least once in a :doc:`pair_coeff <pair_coeff>` command.
.. note::
.. warning::
LAMMPS never performs mixing of parameters from different sub-styles,
**even** if they use the same type of coefficients, e.g. contain
a Lennard-Jones potential variant. Those parameters must be provided
explicitly.
With hybrid pair styles the use of mixing to generate pair
coefficients is significantly limited compared to the individual pair
styles. LAMMPS **never** performs mixing of parameters from
different sub-styles, **even** if they use the same type of
coefficients, e.g. contain a Lennard-Jones potential variant. Those
parameters must be provided explicitly. Also for *hybrid/overlay*
and *hybrid/scaled* mixing is **only** performed for pairs of atom
types for which only a single pair style is assigned.
Thus it is strongly recommended to provide all mixed terms
explicitly. For non-hybrid styles those could be generated and
written out using the :doc:`write_coeff command <write_coeff>` and
then edited as needed to comply with the requirements for hybrid
styles as explained above.
If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the pair of atom types

51
doc/src/pair_lebedeva_z.rst
View File

@ -26,15 +26,29 @@ Examples
Description
"""""""""""
The *lebedeva/z* style computes the Lebedeva interaction
potential as described in :ref:`(Lebedeva et al.) <Leb01>`. An important simplification is made,
which is to take all normals along the z-axis.
The *lebedeva/z* pair style computes the Lebedeva interaction potential
as described in :ref:`(Lebedeva1) <Leb01>` and :ref:`(Lebedeva2)
<Leb02>`. An important simplification is made, which is to take all
normals along the z-axis.
The Lebedeva potential is intended for the description of the interlayer
interaction between graphene layers. To perform a realistic simulation,
this potential must be used in combination with an intralayer potential
such as :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>`
facilitated by using pair style :doc:`hybrid/overlay <pair_hybrid>`. To
keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. This can be achieved by
assigning different atom types to atoms of different layers (e.g. 1 and
2 in the examples above).
Other interactions can be set to zero using pair_style *none*\ .
.. math::
E = & \frac{1}{2} \sum_i \sum_{i \neq j} V_{ij}\\
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij}\\
V_{ij} = & B e^{-\alpha(r_{ij} - z_0)} \\
& + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij} e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
& + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij}) e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
& - A \left(\frac{z_0}{r_ij}\right)^6 + A \left( \frac{z_0}{r_c} \right)^6 \\
\rho^2_{ij} = & x^2_{ij} + y^2_{ij} \qquad (\mathbf{n_i} \equiv \mathbf{\hat{z}})
@ -43,12 +57,15 @@ Energies are shifted so that they go continuously to zero at the cutoff assuming
that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for :math:`V_{ij}` above.
The parameter file (e.g. CC.Lebedeva), is intended for use with metal
:doc:`units <units>`, with energies in meV. An additional parameter, *S*,
is available to facilitate scaling of energies.
The provided parameter file (CC.Lebedeva) contains two sets of parameters.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style *none*\ .
- The first set (element name "C") is suitable for normal conditions and
is taken from :ref:`(Popov1) <Popov>`
- The second set (element name "C1") is suitable for high-pressure
conditions and is taken from :ref:`(Koziol1) <Koziol>`
Both sets contain an additional parameter, *S*, that can be used to
facilitate scaling of energies and is set to 1.0 by default.
Restrictions
""""""""""""
@ -77,4 +94,16 @@ none
.. _Leb01:
**(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
**(Lebedeva1)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
.. _Leb02:
**(Lebedeva2)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
.. _Popov:
**(Popov1)** A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
.. _Koziol:
**(Koziol1)** Z. Koziol, G. Gawlik and J. Jagielski, Chinese Phys. B 28, 096101 (2019).

36
doc/src/pair_local_density.rst
View File

@ -26,23 +26,25 @@ Examples
Description
"""""""""""
The local density (LD) potential is a mean-field manybody potential, and, in some
sense,a generalization of embedded atom models (EAM). The name "local density
potential" arises from the fact that it assigns an energy to an atom depending
on the number of neighboring atoms of given type around it within a predefined
spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
literature suggests that such potentials can be widely useful in capturing
effective multibody forces in a computationally efficient manner so as to
improve the quality of CG models of implicit solvation:ref:`(Sanyal1) <Sanyal1>` and
phase-segregation in liquid mixtures:ref:`(Sanyal2) <Sanyal2>`, and provide guidelines
to determine the extent of manybody correlations present in a CG
model.:ref:`(Rosenberger) <Rosenberger>` The LD potential in LAMMPS is primarily
intended to be used as a corrective potential over traditional pair potentials
in bottom-up CG models, i.e., as a hybrid pair style with
other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
Because the LD potential is not a pair potential per se, it is implemented
simply as a single auxiliary file with all specifications that will be read
upon initialization.
The local density (LD) potential is a mean-field manybody potential,
and, in some way, a generalization of embedded atom models (EAM). The
name "local density potential" arises from the fact that it assigns an
energy to an atom depending on the number of neighboring atoms of a
given type around it within a predefined spherical volume (i.e., within
the cutoff). The bottom-up coarse-graining (CG) literature suggests
that such potentials can be widely useful in capturing effective
multibody forces in a computationally efficient manner and thus improve
the quality of CG models of implicit solvation :ref:`(Sanyal1)
<Sanyal1>` and phase-segregation in liquid mixtures :ref:`(Sanyal2)
<Sanyal2>`, and provide guidelines to determine the extent of manybody
correlations present in a CG model :ref:`(Rosenberger) <Rosenberger>`.
The LD potential in LAMMPS is primarily intended to be used as a
corrective potential over traditional pair potentials in bottom-up CG
models via :doc:`hybrid/overlay pair style <pair_hybrid>` with other
explicit pair interaction terms (e.g., tabulated, Lennard-Jones, Morse
etc.). Because the LD potential is not a pair potential per se, it is
implemented simply as a single auxiliary file with all specifications
that will be read upon initialization.
.. note::

16
doc/src/pair_meam.rst
View File

@ -28,16 +28,16 @@ Description
as of November 2010; see description below of the mixture_ref_t
parameter
Style *meam* computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
Pair style *meam* computes non-bonded interactions for a variety of materials
using the modified embedded-atom method (MEAM)
:ref:`(Baskes) <Baskes>`. Conceptually, it is an extension to the original
:doc:`EAM potentials <pair_eam>` which adds angular forces. It is
:doc:`EAM method <pair_eam>` which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon. Style *meam* is a translation of the (now obsolete)
*meam* code from Fortran to C++. It is functionally equivalent to *meam*
but more efficient, and thus *meam* has been removed from LAMMPS after
the 12 December 2018 release.
diamond cubic structures, as well as materials with covalent interactions
like silicon and carbon. This *meam* pair style is a translation of the
original Fortran version to C++. It is functionally equivalent but more
efficient and has additional features. The Fortran version of the *meam*
pair style has been removed from LAMMPS after the 12 December 2018 release.
In the MEAM formulation, the total energy E of a system of atoms is
given by:

20
doc/src/pair_modify.rst
View File

@ -71,21 +71,23 @@ The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
:doc:`pair_coeff <pair_coeff>` command or in the "Pair Coeffs" section of the
:doc:`data file <read_data>`. For some pair styles it is not
:doc:`pair_coeff <pair_coeff>` command or in the "Pair Coeffs" or "PairIJ Coeffs"
sections of the :doc:`data file <read_data>`. For some pair styles it is not
necessary to specify coefficients when I != J, since a "mixing" rule
will create them from the I,I and J,J settings. The pair_modify
*mix* value determines what formulas are used to compute the mixed
coefficients. In each case, the cutoff distance is mixed the same way
as sigma.
Note that not all pair styles support mixing and some mix options
are not available for certain pair styles. Also, there are additional
restrictions when using :doc:`pair style hybrid or hybrid/overlay <pair_hybrid>`.
See the page for individual pair styles for those restrictions. Note also that the
:doc:`pair_coeff <pair_coeff>` command also can be used to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.
Note that not all pair styles support mixing and some mix options are
not available for certain pair styles. Also, there are additional
restrictions when using :doc:`pair style hybrid or hybrid/overlay
<pair_hybrid>`. See the page for individual pair styles for those
restrictions. Note also that the :doc:`pair_coeff <pair_coeff>` command
also can be used to directly set coefficients for a specific I != J
pairing, in which case no mixing is performed. If possible, LAMMPS will
print an informational message about how many of the mixed pair
coefficients were generated and which mixing rule was applied.
- mix *geometric*

29
doc/src/pair_nm.rst
View File

@ -1,4 +1,5 @@
.. index:: pair_style nm/cut
.. index:: pair_style nm/cut/split
.. index:: pair_style nm/cut/coul/cut
.. index:: pair_style nm/cut/coul/long
.. index:: pair_style nm/cut/omp
@ -10,6 +11,9 @@ pair_style nm/cut command
Accelerator Variants: *nm/cut/omp*
pair_style nm/cut/split command
===============================
pair_style nm/cut/coul/cut command
==================================
@ -27,13 +31,15 @@ Syntax
pair_style style args
* style = *nm/cut* or *nm/cut/coul/cut* or *nm/cut/coul/long*
* style = *nm/cut* or *nm/cut/split* or *nm/cut/coul/cut* or *nm/cut/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*nm/cut* args = cutoff
cutoff = global cutoff for Pair interactions (distance units)
*nm/cut/split* args = cutoff
cutoff = global cutoff for Pair interactions (distance units)
*nm/cut/coul/cut* args = cutoff (cutoff2)
cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -50,6 +56,10 @@ Examples
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/split 1.12246
pair_coeff 1 1 1.0 1.1246 12 6
pair_coeff * * 1.0 1.1246 11 6
pair_style nm/cut/coul/cut 12.0 15.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
@ -71,7 +81,15 @@ interaction has the following form:
E = \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n
\left(\frac{r_0}{r}\right)^m \right] \qquad r < r_c
where :math:`r_c` is the cutoff.
where :math:`r_c` is the cutoff and :math:`r_0` is the minimum of the
potential. Please note that this differs from the convention used for
other Lennard-Jones potentials in LAMMPS where :math:`\sigma` represents
the location where the energy is zero.
Style *nm/cut/split* applies the standard LJ (12-6) potential above
:math:`r_0 = 2^\frac{1}{6}\sigma`. Style *nm/cut/split* is employed in
polymer equilibration protocols that combine core-softening approaches
with topology-changing moves :ref:`Dietz <Dietz>`.
Style *nm/cut/coul/cut* adds a Coulombic pairwise interaction given by
@ -155,7 +173,6 @@ the :doc:`run_style respa <run_style>` command. They do not support the
Restrictions
""""""""""""
These pair styles are part of the EXTRA-PAIR package. They are only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
@ -163,7 +180,7 @@ LAMMPS was built with that package. See the
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair style lj/cut <pair_lj>`, :doc:`bond style fene/nm <bond_fene>`
Default
"""""""
@ -175,3 +192,7 @@ none
.. _Clarke:
**(Clarke)** Clarke and Smith, J Chem Phys, 84, 2290 (1986).
.. _Dietz:
**(Dietz)** Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).

18
doc/src/pair_python.rst
View File

@ -126,11 +126,11 @@ and *compute_energy*, which both take 3 numerical arguments:
* itype = the (numerical) type of the first atom
* jtype = the (numerical) type of the second atom
This functions need to compute the force and the energy, respectively,
and use the result as return value. The functions need to use the
*pmap* dictionary to convert the LAMMPS atom type number to the symbolic
value of the internal potential parameter data structure. Following
the *LJCutMelt* example, here are the two functions:
This functions need to compute the (scaled) force and the energy,
respectively, and use the result as return value. The functions need
to use the *pmap* dictionary to convert the LAMMPS atom type number
to the symbolic value of the internal potential parameter data structure.
Following the *LJCutMelt* example, here are the two functions:
.. code-block:: python
@ -154,10 +154,10 @@ the *LJCutMelt* example, here are the two functions:
for consistency with the C++ pair styles in LAMMPS, the
*compute_force* function follows the conventions of the Pair::single()
methods and does not return the full force, but the force scaled by
the distance between the two atoms, so this value only needs to be
multiplied by delta x, delta y, and delta z to conveniently obtain the
three components of the force vector between these two atoms.
methods and does not return the pairwise force directly, but the force
divided by the distance between the two atoms, so this value only needs
to be multiplied by delta x, delta y, and delta z to conveniently obtain
the three components of the force vector between these two atoms.
----------

2
doc/src/pair_style.rst
View File

@ -274,6 +274,7 @@ accelerated styles exist.
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb
* :doc:`nm/cut/split <pair_nm>` - Split 12-6 Lennard-Jones and N-M potential
* :doc:`oxdna/coaxstk <pair_oxdna>` -
* :doc:`oxdna/excv <pair_oxdna>` -
* :doc:`oxdna/hbond <pair_oxdna>` -
@ -327,6 +328,7 @@ accelerated styles exist.
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -
* :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
* :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential
* :doc:`table <pair_table>` - tabulated pair potential
* :doc:`table/rx <pair_table_rx>` -
* :doc:`tdpd <pair_mesodpd>` - tDPD particle interactions

80
doc/src/pair_sw.rst
View File

@ -3,18 +3,34 @@
.. index:: pair_style sw/intel
.. index:: pair_style sw/kk
.. index:: pair_style sw/omp
.. index:: pair_style sw/mod
.. index:: pair_style sw/mod/omp
pair_style sw command
=====================
Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp*
pair_style sw/mod command
=========================
Accelerator Variants: *sw/mod/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style sw
pair_style style keyword values
* style = *sw* or *sw/mod*
* keyword = *maxdelcs*
.. parsed-literal::
*maxdelcs* value = delta1 delta2 (optional)
delta1 = The minimum thershold for cosine of three-body angle
delta2 = The maximum threshold for cosine of three-body angle
Examples
""""""""
@ -25,6 +41,9 @@ Examples
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
Description
"""""""""""
@ -48,8 +67,52 @@ where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a
three-body term. The summations in the formula are over all neighbors J
and K of atom I within a cutoff distance :math:`a `\sigma`.
Only a single pair_coeff command is used with the *sw* style which
specifies a Stillinger-Weber potential file with parameters for all
The *sw/mod* style is designed for simulations of materials when
distinguishing three-body angles are necessary, such as borophene
and transition metal dichalcogenide, which cannot be described
by the original code for the Stillinger-Weber potential.
For instance, there are several types of angles around each Mo atom in `MoS_2`,
and some unnecessary angle types should be excluded in the three-body interaction.
Such exclusion may be realized by selecting proper angle types directly.
The exclusion of unnecessary angles is achieved here by the cut-off function (`f_C(\delta)`),
which induces only minimum modifications for LAMMPS.
Validation, benchmark tests, and applications of the *sw/mod* style
can be found in :ref:`(Jiang2) <Jiang2>` and :ref:`(Jiang3) <Jiang3>`.
The *sw/mod* style computes the energy E of a system of atoms, whose potential
function is mostly the same as the Stillinger-Weber potential. The only modification
is in the three-body term, where the value of :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}`
used in the original energy and force expression is scaled by a switching factor :math:`f_C(\delta)`:
.. math::
f_C(\delta) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & \left| \delta \right| < \delta_1 \\
\frac{1}{2} + \frac{1}{2} \cos \left( \pi \frac{\left| \delta \right| - \delta_1}{\delta_2 - \delta_1} \right) &
\delta_1 < \left| \delta \right| < \delta_2 \\
0 & \left| \delta \right| > \delta_2
\end{array} \right. \\
This cut-off function decreases smoothly from 1 to 0 over the range :math:`[\delta_1, \delta_2]`.
This smoothly turns off the energy and force contributions for :math:`\left| \delta \right| > \delta_2`.
It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around
:math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with
:math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom.
For borophene and transition metal dichalcogenide, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`.
This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms.
.. note::
The cut-off function is just to be used as a technique to exclude some unnecessary angles,
and it has no physical meaning. It should be noted that the force and potential are inconsistent
with each other in the decaying range of the cut-off function, as the angle dependence for the
cut-off function is not implemented in the force (first derivation of potential).
However, the angle variation is much smaller than the given threshold value for actual simulations,
so the inconsistency between potential and force can be neglected in actual simulations.
Only a single pair_coeff command is used with the *sw* and *sw/mod* styles
which specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
@ -213,10 +276,19 @@ Related commands
Default
"""""""
none
The default values for the *maxdelcs* setting of the *sw/mod* pair
style are *delta1* = 0.25 and *delta2* = 0.35`.
----------
.. _Stillinger2:
**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
.. _Jiang2:
**(Jiang2)** J.-W. Jiang, Nanotechnology 26, 315706 (2015).
.. _Jiang3:
**(Jiang3)** J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).

2
doc/src/pair_tersoff.rst
View File

@ -23,7 +23,7 @@ Syntax
pair_style style keywords values
* style = *tersoff* or *tersoff/table* or *tersoff/gpu* or *tersoff/omp* or *tersoff/table/omp*
* style = *tersoff* or *tersoff/table*
* keyword = *shift*
.. parsed-literal::

4
doc/src/pair_thole.rst
View File

@ -17,7 +17,7 @@ Syntax
pair_style style args
* style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
* style = *thole* or *lj/cut/thole/long*
* args = list of arguments for a particular style
.. parsed-literal::
@ -25,7 +25,7 @@ Syntax
*thole* args = damp cutoff
damp = global damping parameter
cutoff = global cutoff (distance units)
*lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
*lj/cut/thole/long* args = damp cutoff (cutoff2)
damp = global damping parameter
cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
cutoff2 = global cutoff for Thole (optional) (distance units)

6
doc/src/pair_vashishta.rst
View File

@ -22,13 +22,13 @@ Syntax
pair_style style args
* style = *vashishta* or *vashishta/table* or *vashishta/omp* or *vashishta/table/omp*
* style = *vashishta* or *vashishta/table*
* args = list of arguments for a particular style
.. parsed-literal::
*vashishta* or *vashishta/omp* args = none
*vashishta/table* or *vashishta/table/omp* args = Ntable cutinner
*vashishta* args = none
*vashishta/table* args = Ntable cutinner
Ntable = # of tabulation points
cutinner = tablulate from cutinner to cutoff

9
doc/src/read_dump.rst
View File

@ -98,8 +98,7 @@ command, after the dump snapshot is read.
----------
If the dump filename specified as *file* ends with ".gz", the dump
file is read in gzipped format. You cannot (yet) read a dump file
that was written in binary format with a ".bin" suffix.
file is read in gzipped format.
You can read dump files that were written (in parallel) to multiple
files via the "%" wild-card character in the dump file name. If any
@ -115,8 +114,8 @@ to tell LAMMPS how many parallel files exist, via its specified
The format of the dump file is selected through the *format* keyword.
If specified, it must be the last keyword used, since all remaining
arguments are passed on to the dump reader. The *native* format is
for native LAMMPS dump files, written with a :doc:`dump atom <dump>` or
:doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
for native LAMMPS dump files, written with a :doc:`dump atom <dump>`
or :doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
formatted dump files. These formats take no additional values.
The *molfile* format supports reading data through using the `VMD <vmd_>`_
@ -370,8 +369,6 @@ needed to generate absolute, unscaled coordinates.
Restrictions
""""""""""""
The *native* dump file reader does not support binary .bin dump files.
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.

2
doc/utils/requirements.txt
View File

@ -1,6 +1,6 @@
Sphinx
sphinxcontrib-spelling
git+git://github.com/akohlmey/sphinx-fortran@parallel-read
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs
breathe
Pygments

11
doc/utils/sphinx-config/false_positives.txt
View File

@ -308,6 +308,7 @@ boolean
boostostat
boostostatting
Boresch
borophene
Botero
Botu
Bouguet
@ -688,8 +689,10 @@ diagonalizers
diagonalizing
Diallo
diblock
dichalcogenide
Dickel
diel
Dietz
differentiable
diffusively
diffusivity
@ -1125,6 +1128,7 @@ gaussian
gaussians
Gaussians
Gavhane
Gawlik
gayberne
gcc
gcmc
@ -1308,6 +1312,7 @@ hotpink
Houlle
howto
Howto
Hoy
Hoyt
Hs
hstyle
@ -1483,6 +1488,7 @@ Izz
Jacobsen
Jadhao
Jadhav
Jagielski
jagreat
Jahn
Jalalvand
@ -1609,6 +1615,7 @@ Koslowski
Kosovan
Koster
Kosztin
Koziol
Kp
kradius
Kraker
@ -1995,6 +2002,7 @@ minimizer
minimizers
minneigh
minorder
MinSizeRel
minSteps
mintcream
Mintmire
@ -2386,6 +2394,7 @@ ohenrich
ok
Okabe
Okamoto
O'Hearn
O'Keefe
OKeefe
oldlace
@ -2784,6 +2793,7 @@ relink
relres
relTol
relu
RelWithDebInfo
remappings
remd
Ren
@ -3073,6 +3083,7 @@ snav
Snodin
Sodani
Soderlind
Solida
solvated
solvation
someuser

2
examples/ELASTIC_T/potential.mod
View File

@ -1,6 +1,8 @@
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
# we must undefine any fix ave/* fix before using reset_timestep
if "$(is_defined(fix,avp)" then "unfix avp"
reset_timestep 0
# Choose potential

2
examples/PACKAGES/local_density/benzene_water/benzene_water.localdensity.table
View File

@ -1,4 +1,4 @@
# local density potentials: (B,B), (W,W), (B,W), (W,B)
# local density potentials: (B,B), (W,W), (B,W), (W,B) UNITS: real
4 500

2
examples/PACKAGES/local_density/benzene_water/benzene_water.pair.table
View File

@ -1,4 +1,4 @@
# UNITS: real
PairBB
N 500 R 2.00000e-02 1.32500e+01

14
examples/PACKAGES/local_density/benzene_water/benzene_water.in → examples/PACKAGES/local_density/benzene_water/in.benzene_water
View File

@ -11,7 +11,7 @@
# Initialize simulation box
dimension 3
boundary p p p
boundary p p p
units real
atom_style molecular
@ -32,7 +32,7 @@ pair_coeff * * local/density benzene_water.localdensity.table
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
@ -49,14 +49,14 @@ run 5000
# Turn off recentering during production phase
unfix recentering
reset_timestep 0
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
#dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
#dump_modify myDump element B W
#dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
run 1000

267
examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1
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@ -1,267 +0,0 @@
LAMMPS (7 Aug 2019)
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
1 by 1 by 8 MPI processor grid
reading atoms ...
1380 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000566959 secs
read_data CPU = 0.00661397 secs
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 150 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 90 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 135 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 4162.3053 5395.4665 0 0 0 4162.3053
300 1233.1611 2275.526 3508.6871 0 0 0 2275.526
Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
71.3% CPU use with 8 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
4162.30533361 2208.86525108 2275.52597861
Force two-norm initial, final = 259.364 69.3915
Force max component initial, final = 22.2077 8.31436
Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
Iterations, force evaluations = 40 110
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.053192 | 0.23903 | 0.32779 | 17.2 | 67.75
Bond | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 | 0.0 | 0.00
Neigh | 0.00044513 | 0.0023614 | 0.0063851 | 5.1 | 0.67
Comm | 0.015469 | 0.090432 | 0.20295 | 20.0 | 25.63
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02098 | | | 5.95
Nlocal: 172.5 ave 348 max 72 min
Histogram: 5 0 0 0 0 0 0 0 1 2
Nghost: 2193.62 ave 4352 max 932 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 9700.5 ave 20535 max 3685 min
Histogram: 5 0 0 0 0 0 0 1 0 2
Total # of neighbors = 77604
Ave neighs/atom = 56.2348
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2866.9109 4100.0721 0 0 0 2866.9109
273.33541 1123.5553 3983.2007 5106.756 0 0 0 3983.2007
293.68078 1207.1857 3319.6601 4526.8458 0 0 0 3319.6601
314.21462 1291.5908 3389.2178 4680.8086 0 0 0 3389.2178
323.77563 1330.8917 3332.9828 4663.8745 0 0 0 3332.9828
302.5902 1243.8082 3461.7692 4705.5774 0 0 0 3461.7692
295.39324 1214.2249 3411.5727 4625.7976 0 0 0 3411.5727
320.52341 1317.5234 3453.1931 4770.7164 0 0 0 3453.1931
312.00777 1282.5195 3403.3443 4685.8638 0 0 0 3403.3443
307.96774 1265.9128 3429.7809 4695.6937 0 0 0 3429.7809
294.75922 1211.6187 3388.8404 4600.4591 0 0 0 3388.8404
311.24567 1279.3869 3514.9603 4794.3472 0 0 0 3514.9603
306.6152 1260.3531 3447.2011 4707.5542 0 0 0 3447.2011
305.23306 1254.6718 3375.5092 4630.181 0 0 0 3375.5092
321.62889 1322.0675 3460.2581 4782.3256 0 0 0 3460.2581
316.37725 1300.4804 3437.0312 4737.5116 0 0 0 3437.0312
322.90522 1327.3139 3389.1262 4716.44 0 0 0 3389.1262
307.57893 1264.3146 3359.8491 4624.1637 0 0 0 3359.8491
302.22607 1242.3115 3406.1711 4648.4826 0 0 0 3406.1711
302.73997 1244.4239 3220.2582 4464.6821 0 0 0 3220.2582
303.66194 1248.2137 3318.4629 4566.6765 0 0 0 3318.4629
308.73862 1269.0815 3369.5894 4638.671 0 0 0 3369.5894
315.60294 1297.2976 3411.2405 4708.5381 0 0 0 3411.2405
310.0113 1274.3129 3360.1054 4634.4183 0 0 0 3360.1054
302.36229 1242.8714 3326.9845 4569.8559 0 0 0 3326.9845
317.78659 1306.2735 3355.4976 4661.7711 0 0 0 3355.4976
302.50479 1243.4571 3317.6846 4561.1417 0 0 0 3317.6846
304.29249 1250.8056 3423.5068 4674.3124 0 0 0 3423.5068
305.99948 1257.8222 3432.9395 4690.7617 0 0 0 3432.9395
309.93363 1273.9937 3393.657 4667.6506 0 0 0 3393.657
316.14884 1299.5415 3463.0636 4762.6051 0 0 0 3463.0636
300.38817 1234.7567 3309.2495 4544.0062 0 0 0 3309.2495
311.05735 1278.6128 3304.4418 4583.0546 0 0 0 3304.4418
311.11872 1278.865 3291.1891 4570.0542 0 0 0 3291.1891
315.74338 1297.8749 3341.3063 4639.1812 0 0 0 3341.3063
297.5658 1223.1552 3316.3862 4539.5414 0 0 0 3316.3862
311.79033 1281.6257 3357.4556 4639.0813 0 0 0 3357.4556
310.93666 1278.1167 3414.7694 4692.8861 0 0 0 3414.7694
307.37298 1263.468 3337.3889 4600.8569 0 0 0 3337.3889
298.84185 1228.4005 3329.6173 4558.0178 0 0 0 3329.6173
310.54684 1276.5143 3351.0852 4627.5995 0 0 0 3351.0852
300.0871 1233.5191 3302.2315 4535.7506 0 0 0 3302.2315
304.69078 1252.4427 3324.2508 4576.6935 0 0 0 3324.2508
313.50714 1288.6827 3330.4088 4619.0915 0 0 0 3330.4088
329.80018 1355.6559 3301.86 4657.5159 0 0 0 3301.86
304.57609 1251.9713 3365.2938 4617.2652 0 0 0 3365.2938
308.73584 1269.0701 3344.4155 4613.4856 0 0 0 3344.4155
306.90951 1261.5629 3304.4698 4566.0327 0 0 0 3304.4698
308.85761 1269.5707 3392.1511 4661.7218 0 0 0 3392.1511
302.78788 1244.6208 3317.0849 4561.7057 0 0 0 3317.0849
321.68092 1322.2813 3321.5755 4643.8568 0 0 0 3321.5755
Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
69.6% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1872 | 10.542 | 14.607 | 116.7 | 64.65
Bond | 0.00044084 | 0.00069669 | 0.00095081 | 0.0 | 0.00
Neigh | 0.026948 | 0.15225 | 0.44344 | 42.0 | 0.93
Comm | 0.63452 | 4.2953 | 9.49 | 133.9 | 26.34
Output | 0.0016391 | 0.012378 | 0.050919 | 13.9 | 0.08
Modify | 0.45894 | 1.2107 | 4.4629 | 116.4 | 7.42
Other | | 0.09292 | | | 0.57
Nlocal: 172.5 ave 380 max 70 min
Histogram: 5 0 0 0 0 0 0 1 1 1
Nghost: 2213 ave 4440 max 903 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 10042.5 ave 24051 max 3500 min
Histogram: 5 0 0 0 0 0 0 1 1 1
Total # of neighbors = 80340
Ave neighs/atom = 58.2174
Ave special neighs/atom = 0
Neighbor list builds = 123
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
321.68092 1322.2813 3784.0834 5106.3647 0 0 0 3784.0834
310.59763 1276.7231 3318.3283 4595.0513 0 0 0 3318.3283
303.39445 1247.1141 3324.1191 4571.2332 0 0 0 3324.1191
311.37275 1279.9092 3305.0901 4584.9993 0 0 0 3305.0901
311.29071 1279.572 3248.216 4527.788 0 0 0 3248.216
314.53456 1292.906 3283.4563 4576.3623 0 0 0 3283.4563
316.52595 1301.0916 3258.9171 4560.0087 0 0 0 3258.9171
318.92447 1310.9509 3235.6256 4546.5765 0 0 0 3235.6256
311.79212 1281.6331 3308.099 4589.7321 0 0 0 3308.099
305.52477 1255.8709 3267.6907 4523.5616 0 0 0 3267.6907
301.07457 1237.5782 3206.3997 4443.9779 0 0 0 3206.3997
Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
60.8% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.656 | 2.5078 | 3.5775 | 57.7 | 56.46
Bond | 0.00013375 | 0.0001854 | 0.0002377 | 0.0 | 0.00
Neigh | 0.0048757 | 0.029188 | 0.090432 | 18.9 | 0.66
Comm | 0.51836 | 1.4427 | 2.6285 | 56.9 | 32.48
Output | 0.083084 | 0.089199 | 0.10333 | 2.3 | 2.01
Modify | 0.0087376 | 0.019705 | 0.038437 | 8.4 | 0.44
Other | | 0.3526 | | | 7.94
Nlocal: 172.5 ave 388 max 69 min
Histogram: 5 0 0 0 0 0 0 2 0 1
Nghost: 2207.88 ave 4429 max 896 min
Histogram: 3 0 0 2 0 0 2 0 0 1
Neighs: 10094.1 ave 24847 max 3403 min
Histogram: 5 0 0 0 0 0 1 1 0 1
Total # of neighbors = 80753
Ave neighs/atom = 58.5167
Ave special neighs/atom = 0
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:21

300
examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1 Normal file
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@ -0,0 +1,300 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
Reading data file ...
orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
1 by 1 by 1 MPI processor grid
reading atoms ...
1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING: over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2374.6749 3607.836 0 0 0 2374.6749
300 1233.1611 985.54829 2218.7094 0 0 0 985.54829
300 1233.1611 962.66036 2195.8215 0 0 0 962.66036
Loop time of 0.812343 on 1 procs for 134 steps with 1380 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2374.67491482358 962.664796664787 962.660357218268
Force two-norm initial, final = 263.77519 15.741017
Force max component initial, final = 22.412654 7.9360139
Final line search alpha, max atom move = 0.014975513 0.11884588
Iterations, force evaluations = 134 240
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.78539 | 0.78539 | 0.78539 | 0.0 | 96.68
Bond | 2.0149e-05 | 2.0149e-05 | 2.0149e-05 | 0.0 | 0.00
Neigh | 0.016759 | 0.016759 | 0.016759 | 0.0 | 2.06
Comm | 0.0045 | 0.0045 | 0.0045 | 0.0 | 0.55
Output | 2.9402e-05 | 2.9402e-05 | 2.9402e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005647 | | | 0.70
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5832.00 ave 5832 max 5832 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 78165.0 ave 78165 max 78165 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 78165
Ave neighs/atom = 56.641304
Ave special neighs/atom = 0.0000000
Neighbor list builds = 5
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.629 | 7.629 | 7.629 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 962.66036 2195.8215 0 0 0 962.66036
253.1913 1040.7522 1803.711 2844.4633 0 0 0 1803.711
290.31049 1193.332 2059.0637 3252.3958 0 0 0 2059.0637
299.30778 1230.3157 2140.226 3370.5417 0 0 0 2140.226
309.81524 1273.507 2178.3782 3451.8853 0 0 0 2178.3782
299.79526 1232.3195 2229.9248 3462.2444 0 0 0 2229.9248
299.24909 1230.0745 2260.7129 3490.7874 0 0 0 2260.7129
299.5898 1231.475 2244.2384 3475.7134 0 0 0 2244.2384
297.81223 1224.1682 2320.27 3544.4382 0 0 0 2320.27
301.53975 1239.4903 2277.0431 3516.5334 0 0 0 2277.0431
292.00572 1200.3003 2292.3073 3492.6076 0 0 0 2292.3073
309.19709 1270.9661 2303.6055 3574.5716 0 0 0 2303.6055
297.54933 1223.0876 2304.127 3527.2146 0 0 0 2304.127
303.48106 1247.4702 2303.5673 3551.0375 0 0 0 2303.5673
296.46047 1218.6118 2256.1591 3474.7709 0 0 0 2256.1591
299.4835 1231.038 2280.0452 3511.0832 0 0 0 2280.0452
306.25958 1258.8914 2307.9795 3566.8709 0 0 0 2307.9795
304.67335 1252.3711 2284.8252 3537.1963 0 0 0 2284.8252
298.33637 1226.3227 2289.8499 3516.1726 0 0 0 2289.8499
303.1338 1246.0427 2342.2148 3588.2575 0 0 0 2342.2148
305.86051 1257.251 2341.0106 3598.2616 0 0 0 2341.0106
297.75418 1223.9296 2303.5613 3527.4909 0 0 0 2303.5613
296.79348 1219.9806 2327.5207 3547.5013 0 0 0 2327.5207
307.25403 1262.9791 2288.4219 3551.401 0 0 0 2288.4219
301.26976 1238.3805 2291.2465 3529.627 0 0 0 2291.2465
297.17249 1221.5385 2283.3926 3504.9311 0 0 0 2283.3926
313.99072 1290.6705 2293.9661 3584.6366 0 0 0 2293.9661
301.70804 1240.1821 2331.1694 3571.3515 0 0 0 2331.1694
300.62599 1235.7343 2325.4367 3561.171 0 0 0 2325.4367
292.13495 1200.8316 2315.631 3516.4626 0 0 0 2315.631
313.9981 1290.7008 2286.0536 3576.7545 0 0 0 2286.0536
300.25311 1234.2015 2324.2379 3558.4394 0 0 0 2324.2379
309.3746 1271.6958 2322.2298 3593.9256 0 0 0 2322.2298
300.23041 1234.1082 2332.7521 3566.8603 0 0 0 2332.7521
302.97054 1245.3716 2303.1689 3548.5405 0 0 0 2303.1689
294.77155 1211.6694 2334.5087 3546.1781 0 0 0 2334.5087
296.81476 1220.0681 2322.5932 3542.6613 0 0 0 2322.5932
301.83238 1240.6932 2345.4841 3586.1773 0 0 0 2345.4841
295.0399 1212.7724 2312.3889 3525.1614 0 0 0 2312.3889
300.73565 1236.185 2338.8384 3575.0235 0 0 0 2338.8384
303.02264 1245.5858 2310.0868 3555.6726 0 0 0 2310.0868
302.86404 1244.9339 2332.2001 3577.134 0 0 0 2332.2001
293.77916 1207.5901 2293.2799 3500.8701 0 0 0 2293.2799
299.30072 1230.2867 2317.5065 3547.7933 0 0 0 2317.5065
311.05029 1278.5837 2311.0476 3589.6313 0 0 0 2311.0476
293.25646 1205.4416 2314.7398 3520.1814 0 0 0 2314.7398
310.49018 1276.2814 2337.4909 3613.7723 0 0 0 2337.4909
302.37336 1242.9169 2340.3197 3583.2366 0 0 0 2340.3197
297.06862 1221.1116 2323.9136 3545.0252 0 0 0 2323.9136
300.54817 1235.4144 2315.2405 3550.6549 0 0 0 2315.2405
309.10643 1270.5934 2333.1848 3603.7783 0 0 0 2333.1848
Loop time of 15.2696 on 1 procs for 5000 steps with 1380 atoms
Performance: 56.583 ns/day, 0.424 hours/ns, 327.447 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.432 | 14.432 | 14.432 | 0.0 | 94.51
Bond | 0.00032375 | 0.00032375 | 0.00032375 | 0.0 | 0.00
Neigh | 0.41541 | 0.41541 | 0.41541 | 0.0 | 2.72
Comm | 0.0975 | 0.0975 | 0.0975 | 0.0 | 0.64
Output | 0.0013044 | 0.0013044 | 0.0013044 | 0.0 | 0.01
Modify | 0.30336 | 0.30336 | 0.30336 | 0.0 | 1.99
Other | | 0.01973 | | | 0.13
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5843.00 ave 5843 max 5843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 76949.0 ave 76949 max 76949 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 76949
Ave neighs/atom = 55.760145
Ave special neighs/atom = 0.0000000
Neighbor list builds = 121
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.022 | 9.022 | 9.022 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
309.10643 1270.5934 2333.1848 3603.7783 0 0 0 2333.1848
300.84572 1236.6375 2331.3493 3567.9868 0 0 0 2331.3493
300.90599 1236.8852 2337.6775 3574.5627 0 0 0 2337.6775
302.77895 1244.5841 2341.7778 3586.362 0 0 0 2341.7778
291.66639 1198.9055 2320.3512 3519.2567 0 0 0 2320.3512
298.7003 1227.8187 2292.8195 3520.6382 0 0 0 2292.8195
301.11163 1237.7305 2310.017 3547.7475 0 0 0 2310.017
305.22515 1254.6393 2315.1355 3569.7748 0 0 0 2315.1355
295.15921 1213.2629 2310.184 3523.4468 0 0 0 2310.184
299.2024 1229.8826 2332.2118 3562.0943 0 0 0 2332.2118
302.80078 1244.6738 2320.3763 3565.0502 0 0 0 2320.3763
Loop time of 3.07208 on 1 procs for 1000 steps with 1380 atoms
Performance: 56.249 ns/day, 0.427 hours/ns, 325.512 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8993 | 2.8993 | 2.8993 | 0.0 | 94.37
Bond | 6.5327e-05 | 6.5327e-05 | 6.5327e-05 | 0.0 | 0.00
Neigh | 0.083502 | 0.083502 | 0.083502 | 0.0 | 2.72
Comm | 0.019967 | 0.019967 | 0.019967 | 0.0 | 0.65
Output | 0.012268 | 0.012268 | 0.012268 | 0.0 | 0.40
Modify | 0.052801 | 0.052801 | 0.052801 | 0.0 | 1.72
Other | | 0.004203 | | | 0.14
Nlocal: 1380.00 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5860.00 ave 5860 max 5860 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 77055.0 ave 77055 max 77055 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 77055
Ave neighs/atom = 55.836957
Ave special neighs/atom = 0.0000000
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:19

299
examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4 Normal file
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@ -0,0 +1,299 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data benzene_water.data
Reading data file ...
orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
1 by 1 by 4 MPI processor grid
reading atoms ...
1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
velocity all create 3.0000e+02 16611 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table benzene_water.pair.table PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff 1 2 table benzene_water.pair.table PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING: over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff 2 2 table benzene_water.pair.table PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING: over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density benzene_water.localdensity.table
# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
# Thermostat & time integration
timestep 2.0
thermo 100
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
# Minimization
minimize 1.e-4 0.0 10000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.25
ghost atom cutoff = 15.25
binsize = 7.625, bins = 4 4 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.441 | 8.589 | 8.688 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 2374.6749 3607.836 0 0 0 2374.6749
300 1233.1611 1024.8113 2257.9724 0 0 0 1024.8113
Loop time of 0.240559 on 4 procs for 74 steps with 1380 atoms
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2374.67491482358 1024.89407898645 1024.81130011575
Force two-norm initial, final = 263.77519 20.459697
Force max component initial, final = 22.412654 8.6082349
Final line search alpha, max atom move = 0.027790997 0.23923143
Iterations, force evaluations = 74 118
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15928 | 0.1873 | 0.22814 | 6.5 | 77.86
Bond | 3.857e-06 | 4.4012e-06 | 5.496e-06 | 0.0 | 0.00
Neigh | 0.00064142 | 0.0028761 | 0.0058864 | 4.2 | 1.20
Comm | 0.0040776 | 0.039595 | 0.074187 | 12.6 | 16.46
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01078 | | | 4.48
Nlocal: 345.000 ave 664 max 147 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 2850.50 ave 4438 max 1208 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19377.5 ave 37718 max 7456 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 77510
Ave neighs/atom = 56.166667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 3
Dangerous builds = 0
# Set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep 0
run 5000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.465 | 7.563 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
300 1233.1611 1024.8113 2257.9724 0 0 0 1024.8113
263.61917 1083.6164 1866.745 2950.3614 0 0 0 1866.745
296.0253 1216.823 2122.8463 3339.6692 0 0 0 2122.8463
301.93846 1241.1292 2172.9802 3414.1095 0 0 0 2172.9802
293.9491 1208.2887 2205.4892 3413.7779 0 0 0 2205.4892
286.33795 1177.0027 2204.8908 3381.8935 0 0 0 2204.8908
295.48217 1214.5904 2230.8849 3445.4753 0 0 0 2230.8849
293.88908 1208.0419 2218.7563 3426.7982 0 0 0 2218.7563
295.13798 1213.1756 2277.4515 3490.6271 0 0 0 2277.4515
290.39538 1193.681 2273.4385 3467.1195 0 0 0 2273.4385
297.56782 1223.1635 2268.7182 3491.8817 0 0 0 2268.7182
306.45578 1259.6978 2289.1507 3548.8486 0 0 0 2289.1507
308.54582 1268.289 2284.8514 3553.1404 0 0 0 2284.8514
302.17353 1242.0955 2262.5577 3504.6532 0 0 0 2262.5577
295.30087 1213.8452 2315.8853 3529.7305 0 0 0 2315.8853
308.59197 1268.4787 2291.8314 3560.3101 0 0 0 2291.8314
297.75618 1223.9378 2287.2003 3511.1381 0 0 0 2287.2003
303.43395 1247.2765 2297.7158 3544.9923 0 0 0 2297.7158
307.16233 1262.6021 2255.9769 3518.5791 0 0 0 2255.9769
301.34428 1238.6868 2284.416 3523.1028 0 0 0 2284.416
295.43209 1214.3846 2294.1043 3508.4889 0 0 0 2294.1043
287.86904 1183.2963 2257.0204 3440.3168 0 0 0 2257.0204
297.2661 1221.9233 2251.4194 3473.3428 0 0 0 2251.4194
298.90221 1228.6486 2261.834 3490.4826 0 0 0 2261.834
288.07202 1184.1307 2284.1918 3468.3225 0 0 0 2284.1918
300.41201 1234.8547 2303.9573 3538.812 0 0 0 2303.9573
283.91279 1167.034 2329.7936 3496.8277 0 0 0 2329.7936
297.27507 1221.9602 2337.0516 3559.0118 0 0 0 2337.0516
296.22263 1217.6341 2335.6424 3553.2765 0 0 0 2335.6424
296.13784 1217.2856 2364.7034 3581.989 0 0 0 2364.7034
308.17642 1266.7706 2320.2753 3587.0459 0 0 0 2320.2753
310.26592 1275.3596 2301.9318 3577.2914 0 0 0 2301.9318
292.97391 1204.2801 2289.8116 3494.0917 0 0 0 2289.8116
294.81231 1211.8369 2315.0388 3526.8757 0 0 0 2315.0388
298.66155 1227.6594 2317.2844 3544.9437 0 0 0 2317.2844
302.77939 1244.5859 2301.2063 3545.7922 0 0 0 2301.2063
291.47597 1198.1228 2285.1757 3483.2985 0 0 0 2285.1757
286.19045 1176.3964 2265.2665 3441.6629 0 0 0 2265.2665
295.58144 1214.9984 2272.3165 3487.315 0 0 0 2272.3165
283.86988 1166.8577 2320.6142 3487.4719 0 0 0 2320.6142
300.0576 1233.3979 2330.8962 3564.2941 0 0 0 2330.8962
299.86413 1232.6026 2321.2281 3553.8308 0 0 0 2321.2281
292.79017 1203.5248 2334.2308 3537.7557 0 0 0 2334.2308
291.5027 1198.2327 2335.2119 3533.4446 0 0 0 2335.2119
299.55471 1231.3307 2332.5216 3563.8524 0 0 0 2332.5216
293.29613 1205.6046 2295.3263 3500.9309 0 0 0 2295.3263
303.13151 1246.0333 2310.0548 3556.0881 0 0 0 2310.0548
298.83954 1228.391 2297.3117 3525.7027 0 0 0 2297.3117
297.44775 1222.67 2307.2483 3529.9183 0 0 0 2307.2483
309.59874 1272.6171 2309.2439 3581.861 0 0 0 2309.2439
307.47844 1263.9015 2274.998 3538.8995 0 0 0 2274.998
Loop time of 11.2235 on 4 procs for 5000 steps with 1380 atoms
Performance: 76.982 ns/day, 0.312 hours/ns, 445.495 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.1444 | 8.5074 | 10.534 | 44.9 | 75.80
Bond | 0.00017048 | 0.00020672 | 0.00030488 | 0.0 | 0.00
Neigh | 0.026174 | 0.12108 | 0.26052 | 28.2 | 1.08
Comm | 0.21788 | 1.8597 | 3.3375 | 81.2 | 16.57
Output | 0.0008989 | 0.0069895 | 0.021647 | 10.2 | 0.06
Modify | 0.19418 | 0.7044 | 2.1378 | 98.6 | 6.28
Other | | 0.02368 | | | 0.21
Nlocal: 345.000 ave 678 max 148 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 2854.25 ave 4464 max 1181 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19366.8 ave 38533 max 7481 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 77467
Ave neighs/atom = 56.135507
Ave special neighs/atom = 0.0000000
Neighbor list builds = 121
Dangerous builds = 1
# Turn off recentering during production phase
unfix recentering
# Setup trajectory output
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify myDump element B W
dump_modify myDump sort id
# Production (for realistic results, run for 10000000 steps)
reset_timestep 0
run 1000
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.640 | 8.791 | 8.894 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
307.47844 1263.9015 2274.998 3538.8995 0 0 0 2274.998
309.46142 1272.0526 2274.8499 3546.9026 0 0 0 2274.8499
300.70977 1236.0787 2301.0588 3537.1374 0 0 0 2301.0588
300.53659 1235.3668 2316.1008 3551.4675 0 0 0 2316.1008
300.48582 1235.1581 2296.3009 3531.459 0 0 0 2296.3009
299.2618 1230.1267 2325.7501 3555.8768 0 0 0 2325.7501
303.00905 1245.5299 2321.8238 3567.3537 0 0 0 2321.8238
300.07018 1233.4496 2339.2833 3572.7329 0 0 0 2339.2833
304.20292 1250.4374 2353.1018 3603.5392 0 0 0 2353.1018
304.19487 1250.4043 2334.5087 3584.913 0 0 0 2334.5087
294.24283 1209.4961 2335.0535 3544.5496 0 0 0 2335.0535
Loop time of 2.90512 on 4 procs for 1000 steps with 1380 atoms
Performance: 59.481 ns/day, 0.403 hours/ns, 344.220 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8627 | 2.2082 | 2.7289 | 22.6 | 76.01
Bond | 4.042e-05 | 5.3677e-05 | 8.4044e-05 | 0.0 | 0.00
Neigh | 0.0066184 | 0.030172 | 0.064523 | 13.9 | 1.04
Comm | 0.05914 | 0.51145 | 0.86887 | 40.7 | 17.61
Output | 0.0057814 | 0.0073478 | 0.011158 | 2.6 | 0.25
Modify | 0.0085337 | 0.020869 | 0.042248 | 9.4 | 0.72
Other | | 0.127 | | | 4.37
Nlocal: 345.000 ave 682 max 147 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 2836.25 ave 4427 max 1175 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 19249.8 ave 38683 max 7433 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 76999
Ave neighs/atom = 55.796377
Ave special neighs/atom = 0.0000000
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:14

17
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.in → examples/PACKAGES/local_density/methanol_implicit_water/in.methanol_implicit_water
View File

@ -1,6 +1,6 @@
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
@ -9,7 +9,7 @@
# Initialize simulation box
dimension 3
boundary p p p
boundary p p p
units real
atom_style molecular
@ -17,7 +17,7 @@ atom_style molecular
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
read_data methanol_implicit_water.data
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
@ -31,7 +31,7 @@ pair_coeff * * local/density methanol_implicit_water.localdensity.t
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
@ -52,15 +52,14 @@ run 2000
#turn off recentering during production run
unfix recentering
reset_timestep 0
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
#dump_modify myDump element M
#dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000

226
examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1
View File

@ -1,226 +0,0 @@
LAMMPS (7 Aug 2019)
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
2 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00063014 secs
read_data CPU = 0.00599909 secs
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:483)
WARNING: 254 of 500 distance values in table with relative error
over 1e-06 to re-computed values (../pair_table.cpp:492)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1470.3564 2234.7133 -764.35689 300 -764.35689
46.496766 2234.7133 -2188.2165 300 -2188.2165
7.9030246 2234.7133 -2226.8103 300 -2226.8103
Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
91.4% CPU use with 8 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-764.356892369 -2227.85589084 -2226.81026984
Force two-norm initial, final = 134.911 3.83896
Force max component initial, final = 14.1117 1.07422
Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
Iterations, force evaluations = 121 154
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41442 | 0.41976 | 0.42434 | 0.5 | 90.47
Bond | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 | 0.0 | 0.00
Neigh | 0.0084722 | 0.0090862 | 0.010038 | 0.5 | 1.96
Comm | 0.022712 | 0.028157 | 0.034072 | 1.9 | 6.07
Output | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006937 | | | 1.50
Nlocal: 312.5 ave 333 max 299 min
Histogram: 2 2 0 0 1 0 2 0 0 1
Nghost: 2546 ave 2580 max 2517 min
Histogram: 1 1 0 3 0 1 0 0 0 2
Neighs: 33215.4 ave 37251 max 29183 min
Histogram: 1 0 0 1 2 2 0 1 0 1
Total # of neighbors = 265723
Ave neighs/atom = 106.289
Ave special neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
TotEng KinEng PotEng Temp E_vdwl
177.26822 2234.7133 -2057.4451 300 -2057.4451
736.24287 2151.2608 -1415.0179 288.79688 -1415.0179
963.07617 2090.6433 -1127.5671 280.65926 -1127.5671
1148.9049 2173.1327 -1024.2279 291.73309 -1024.2279
1303.6409 2279.8586 -976.21767 306.06055 -976.21767
1355.42 2281.0383 -925.61826 306.21892 -925.61826
1394.5206 2276.2093 -881.68863 305.57064 -881.68863
1346.9764 2215.2973 -868.32091 297.3935 -868.32091
1381.3654 2248.8061 -867.44063 301.89189 -867.44063
1315.8059 2189.3193 -873.51332 293.90606 -873.51332
1314.4456 2209.7431 -895.29752 296.64787 -895.29752
Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
80.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2693 | 5.3572 | 5.457 | 2.1 | 83.84
Bond | 0.00028825 | 0.00033835 | 0.00039148 | 0.0 | 0.01
Neigh | 0.0296 | 0.032337 | 0.035071 | 0.9 | 0.51
Comm | 0.64679 | 0.73397 | 0.80847 | 5.2 | 11.49
Output | 0.00033498 | 0.00051582 | 0.0015228 | 0.0 | 0.01
Modify | 0.16395 | 0.18919 | 0.21056 | 3.9 | 2.96
Other | | 0.07636 | | | 1.19
Nlocal: 312.5 ave 337 max 295 min
Histogram: 2 2 0 1 0 0 0 1 1 1
Nghost: 2551.62 ave 2582 max 2525 min
Histogram: 2 1 0 0 1 1 1 0 1 1
Neighs: 33241.8 ave 37659 max 29705 min
Histogram: 2 0 0 2 2 0 0 0 1 1
Total # of neighbors = 265934
Ave neighs/atom = 106.374
Ave special neighs/atom = 0
Neighbor list builds = 21
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1442.5428 2209.7431 -767.20027 296.64787 -767.20027
1391.8624 2262.6889 -870.82656 303.7556 -870.82656
1375.914 2244.6176 -868.7036 301.3296 -868.7036
1345.9064 2227.2324 -881.32599 298.99573 -881.32599
1379.2334 2278.1156 -898.88222 305.82657 -898.88222
1389.7928 2255.8062 -866.01341 302.83163 -866.01341
1380.4549 2258.2108 -877.75582 303.15443 -877.75582
1380.8489 2256.9432 -876.09428 302.98426 -876.09428
1326.5151 2225.7408 -899.22577 298.79549 -899.22577
1376.6025 2253.0128 -876.41028 302.45662 -876.41028
1331.0008 2218.1033 -887.10258 297.77019 -887.10258
Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
89.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.635 | 21.916 | 22.237 | 3.9 | 86.08
Bond | 0.0011308 | 0.0013149 | 0.0016932 | 0.5 | 0.01
Neigh | 0.14593 | 0.15675 | 0.16667 | 1.9 | 0.62
Comm | 1.3789 | 1.7502 | 1.9558 | 13.7 | 6.87
Output | 0.34664 | 0.82927 | 1.2013 | 32.8 | 3.26
Modify | 0.24904 | 0.25842 | 0.26907 | 1.2 | 1.02
Other | | 0.5475 | | | 2.15
Nlocal: 312.5 ave 327 max 298 min
Histogram: 2 0 0 1 1 0 1 1 1 1
Nghost: 2575 ave 2601 max 2559 min
Histogram: 2 0 3 1 0 0 0 0 1 1
Neighs: 33223.2 ave 35920 max 30303 min
Histogram: 1 1 1 1 0 1 0 0 0 3
Total # of neighbors = 265786
Ave neighs/atom = 106.314
Ave special neighs/atom = 0
Neighbor list builds = 103
Dangerous builds = 0
Total wall time: 0:00:32

259
examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1 Normal file
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@ -0,0 +1,259 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
Reading data file ...
orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
1 by 1 by 1 MPI processor grid
reading atoms ...
2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.016 seconds
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING: over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.535 | 9.535 | 9.535 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1283.8556 2234.7133 -950.85771 300 -950.85771
-10.187232 2234.7133 -2244.9005 300 -2244.9005
-124.79406 2234.7133 -2359.5074 300 -2359.5074
-126.7619 2234.7133 -2361.4752 300 -2361.4752
Loop time of 3.74581 on 1 procs for 205 steps with 2500 atoms
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-950.857712502514 -2361.24417962983 -2361.47519428972
Force two-norm initial, final = 135.25170 2.8038329
Force max component initial, final = 14.083102 1.1154133
Final line search alpha, max atom move = 0.16981022 0.18940857
Iterations, force evaluations = 205 223
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5678 | 3.5678 | 3.5678 | 0.0 | 95.25
Bond | 7.5831e-05 | 7.5831e-05 | 7.5831e-05 | 0.0 | 0.00
Neigh | 0.12962 | 0.12962 | 0.12962 | 0.0 | 3.46
Comm | 0.019204 | 0.019204 | 0.019204 | 0.0 | 0.51
Output | 0.00023948 | 0.00023948 | 0.00023948 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02886 | | | 0.77
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6729.00 ave 6729 max 6729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265637.0 ave 265637 max 265637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265637
Ave neighs/atom = 106.25480
Ave special neighs/atom = 0.0000000
Neighbor list builds = 11
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 8.410 | 8.410 | 8.410 Mbytes
TotEng KinEng PotEng Temp E_vdwl
-126.7619 2234.7133 -2361.4752 300 -2361.4752
517.05047 2015.8636 -1498.8131 270.62043 -1498.8131
931.78263 2135.4332 -1203.6506 286.6721 -1203.6506
1162.6209 2242.1662 -1079.5453 301.00051 -1079.5453
1164.2129 2211.6204 -1047.4075 296.89989 -1047.4075
1258.0085 2286.5942 -1028.5857 306.96477 -1028.5857
1231.1937 2200.814 -969.62032 295.44917 -969.62032
1251.2144 2245.0533 -993.83885 301.3881 -993.83885
1237.2495 2239.8802 -1002.6307 300.69363 -1002.6307
1232.3342 2224.3415 -992.00722 298.60763 -992.00722
1235.3228 2197.191 -961.86817 294.9628 -961.86817
Loop time of 23.6478 on 1 procs for 2000 steps with 2500 atoms
Performance: 7.307 ns/day, 3.284 hours/ns, 84.575 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 | 22.797 | 22.797 | 22.797 | 0.0 | 96.40
Bond | 0.00070412 | 0.00070412 | 0.00070412 | 0.0 | 0.00
Neigh | 0.2249 | 0.2249 | 0.2249 | 0.0 | 0.95
Comm | 0.12259 | 0.12259 | 0.12259 | 0.0 | 0.52
Output | 0.00088925 | 0.00088925 | 0.00088925 | 0.0 | 0.00
Modify | 0.46447 | 0.46447 | 0.46447 | 0.0 | 1.96
Other | | 0.03711 | | | 0.16
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6752.00 ave 6752 max 6752 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265940.0 ave 265940 max 265940 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265940
Ave neighs/atom = 106.37600
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.918 | 9.918 | 9.918 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1235.3228 2197.191 -961.86817 294.9628 -961.86817
1289.8463 2236.1425 -946.29622 300.19186 -946.29622
1348.0825 2305.0295 -956.94703 309.43963 -956.94703
1279.5478 2241.1582 -961.61041 300.86521 -961.61041
1231.8597 2201.9591 -970.09949 295.60291 -970.09949
1277.3424 2221.3696 -944.02725 298.20867 -944.02725
1296.0116 2222.0998 -926.08818 298.3067 -926.08818
1266.2849 2206.3727 -940.08782 296.1954 -940.08782
1313.2808 2260.5077 -947.22683 303.46278 -947.22683
1309.3076 2234.3895 -925.08198 299.95654 -925.08198
1275.9792 2221.3037 -945.32449 298.19982 -945.32449
Loop time of 67.3224 on 1 procs for 10000 steps with 2500 atoms
Performance: 12.834 ns/day, 1.870 hours/ns, 148.539 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 64.476 | 64.476 | 64.476 | 0.0 | 95.77
Bond | 0.0014504 | 0.0014504 | 0.0014504 | 0.0 | 0.00
Neigh | 0.71333 | 0.71333 | 0.71333 | 0.0 | 1.06
Comm | 0.32846 | 0.32846 | 0.32846 | 0.0 | 0.49
Output | 0.46997 | 0.46997 | 0.46997 | 0.0 | 0.70
Modify | 1.2336 | 1.2336 | 1.2336 | 0.0 | 1.83
Other | | 0.09996 | | | 0.15
Nlocal: 2500.00 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6662.00 ave 6662 max 6662 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 265774.0 ave 265774 max 265774 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265774
Ave neighs/atom = 106.30960
Ave special neighs/atom = 0.0000000
Neighbor list builds = 104
Dangerous builds = 0
Total wall time: 0:01:34

259
examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4 Normal file
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@ -0,0 +1,259 @@
LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
# Initialize simulation box
dimension 3
boundary p p p
units real
atom_style molecular
# Set potential styles
pair_style hybrid/overlay table spline 500 local/density
# Read molecule data and set initial velocities
read_data methanol_implicit_water.data
Reading data file ...
orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
1 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
velocity all create 3.0000e+02 12142 rot yes dist gaussian
# Assign potentials
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING: over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff * * local/density methanol_implicit_water.localdensity.table
#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box
#Thermostat & time integration
timestep 1.0
thermo 100
thermo_style custom etotal ke pe temp evdwl
#minimization
minimize 1.e-4 0.0 1000 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair_style local/density command:
@Article{Sanyal16,
author = {T.Sanyal and M.Scott Shell},
title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
journal = {J.~Chem.~Phys.},
year = 2016,
DOI = doi.org/10.1063/1.4958629}
@Article{Sanyal18,
author = {T.Sanyal and M.Scott Shell},
title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
journal = {J.~Phys.~Chem. B},
year = 2018,
DOI = doi.org/10.1021/acs.jpcb.7b12446}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair local/density, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1283.8556 2234.7133 -950.85771 300 -950.85771
-10.187232 2234.7133 -2244.9005 300 -2244.9005
-124.3661 2234.7133 -2359.0794 300 -2359.0794
-146.7158 2234.7133 -2381.4291 300 -2381.4291
Loop time of 0.528503 on 4 procs for 244 steps with 2500 atoms
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-950.857712502527 -2381.2294195605 -2381.42909821383
Force two-norm initial, final = 135.25170 2.3117934
Force max component initial, final = 14.083102 0.60833889
Final line search alpha, max atom move = 0.18347073 0.11161238
Iterations, force evaluations = 244 278
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48518 | 0.48843 | 0.49223 | 0.4 | 92.42
Bond | 1.0084e-05 | 1.0861e-05 | 1.1483e-05 | 0.0 | 0.00
Neigh | 0.018199 | 0.019153 | 0.020036 | 0.5 | 3.62
Comm | 0.010229 | 0.014832 | 0.018994 | 2.6 | 2.81
Output | 3.7985e-05 | 4.2069e-05 | 5.3874e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006032 | | | 1.14
Nlocal: 625.000 ave 638 max 618 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 3613.75 ave 3640 max 3580 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 66411.2 ave 70713 max 62416 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 265645
Ave neighs/atom = 106.25800
Ave special neighs/atom = 0.0000000
Neighbor list builds = 13
Dangerous builds = 0
#set up integration parameters
fix timeintegration all nve
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
#Equilibration (for realistic results, run for 2000000 steps)
reset_timestep 0
thermo 200
thermo_style custom etotal ke pe temp evdwl
#run equilibration
run 2000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.731 Mbytes
TotEng KinEng PotEng Temp E_vdwl
-146.7158 2234.7133 -2381.4291 300 -2381.4291
540.68168 2041.44 -1500.7584 274.05395 -1500.7584
945.4949 2163.7509 -1218.256 290.47363 -1218.256
1118.7729 2195.7579 -1076.985 294.77042 -1076.985
1215.0058 2233.2445 -1018.2387 299.80282 -1018.2387
1251.8045 2240.8439 -989.03944 300.823 -989.03944
1206.649 2149.5807 -942.93169 288.57134 -942.93169
1290.6111 2248.3623 -957.75117 301.83231 -957.75117
1312.8944 2219.147 -906.25264 297.9103 -906.25264
1260.002 2211.4176 -951.41561 296.87266 -951.41561
1335.0956 2270.1367 -935.04108 304.75543 -935.04108
Loop time of 3.56721 on 4 procs for 2000 steps with 2500 atoms
Performance: 48.441 ns/day, 0.495 hours/ns, 560.663 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3122 | 3.3399 | 3.3633 | 1.0 | 93.63
Bond | 7.5941e-05 | 8.062e-05 | 8.7627e-05 | 0.0 | 0.00
Neigh | 0.03524 | 0.036666 | 0.037864 | 0.6 | 1.03
Comm | 0.080116 | 0.10444 | 0.13373 | 6.1 | 2.93
Output | 0.00019977 | 0.00022502 | 0.00029007 | 0.0 | 0.01
Modify | 0.077781 | 0.078206 | 0.078752 | 0.1 | 2.19
Other | | 0.007641 | | | 0.21
Nlocal: 625.000 ave 637 max 616 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 3597.25 ave 3610 max 3586 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 66468.2 ave 69230 max 62721 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 265873
Ave neighs/atom = 106.34920
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0
#turn off recentering during production run
unfix recentering
#setup trajectory output
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify myDump element M
dump_modify myDump sort id
#run production (for realistic results, run for 10000000 steps)
reset_timestep 0
thermo 1000
thermo_style custom etotal ke pe temp evdwl
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes
TotEng KinEng PotEng Temp E_vdwl
1335.0956 2270.1367 -935.04108 304.75543 -935.04108
1266.2305 2227.2123 -960.98186 298.99303 -960.98186
1304.2289 2238.1343 -933.90544 300.45925 -933.90544
1311.3201 2232.0862 -920.7661 299.64733 -920.7661
1289.9028 2241.3533 -951.45049 300.89139 -951.45049
1314.2234 2244.8514 -930.62797 301.361 -930.62797
1282.2744 2240.6716 -958.39719 300.79987 -958.39719
1239.302 2181.5711 -942.2691 292.86591 -942.2691
1327.0954 2242.6441 -915.54875 301.06468 -915.54875
1334.9799 2239.6841 -904.70423 300.66731 -904.70423
1320.6105 2263.4912 -942.88066 303.8633 -942.88066
Loop time of 23.3399 on 4 procs for 10000 steps with 2500 atoms
Performance: 37.018 ns/day, 0.648 hours/ns, 428.451 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.343 | 21.606 | 21.766 | 3.7 | 92.57
Bond | 0.00045963 | 0.0004817 | 0.0005083 | 0.0 | 0.00
Neigh | 0.20708 | 0.22081 | 0.22733 | 1.7 | 0.95
Comm | 0.63014 | 0.80326 | 1.0801 | 19.8 | 3.44
Output | 0.11791 | 0.14443 | 0.22211 | 11.8 | 0.62
Modify | 0.37291 | 0.389 | 0.41719 | 2.7 | 1.67
Other | | 0.1761 | | | 0.75
Nlocal: 625.000 ave 636 max 613 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 3597.00 ave 3613 max 3580 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 66408.5 ave 69186 max 61728 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 265634
Ave neighs/atom = 106.25360
Ave special neighs/atom = 0.0000000
Neighbor list builds = 102
Dangerous builds = 0
Total wall time: 0:00:27

2
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table
View File

@ -1,4 +1,4 @@
#LOCAL DENSITY POTENTIALS
#LOCAL DENSITY POTENTIALS UNITS: real
1 500

2
examples/PACKAGES/local_density/methanol_implicit_water/methanol_implicit_water.pair.table
View File

@ -1,4 +1,4 @@
# UNITS: real
PairMM
N 500 R 2.00000e-02 1.50000e+01

54
examples/plugins/CMakeLists.txt
View File

@ -14,26 +14,29 @@ endif()
project(plugins VERSION 1.0 LANGUAGES CXX)
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# 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)
# when this file is included as subdirectory in the LAMMPS build, many settings are directly imported
if(LAMMPS_DIR)
set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR})
else()
# 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()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
endif()
# C++11 is required
@ -45,9 +48,11 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfaceCXX)
if(NOT LAMMPS_DIR)
include(LAMMPSInterfaceCXX)
endif()
##########################
# building the plugins
@ -66,7 +71,7 @@ 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 "")
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES PREFIX "" SUFFIX ".so")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
@ -84,3 +89,6 @@ else()
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
LINK_FLAGS "-rdynamic")
endif()
add_custom_target(plugins ALL ${CMAKE_COMMAND} -E echo "Building Plugins"
DEPENDS morse2plugin nve2plugin helloplugin zero2plugin morse2plugin)

30
examples/threebody/in.mos2.sw.mod Normal file
View File

@ -0,0 +1,30 @@
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style atomic
read_data single_layer_MoS2.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000

92
examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 Normal file
View File

@ -0,0 +1,92 @@
LAMMPS (27 Oct 2021)
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style atomic
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
768 atoms
read_data CPU = 0.043 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.158796
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.466 | 3.466 | 3.466 Mbytes
Step TotEng PotEng KinEng Temp
0 -899.28605 -929.02881 29.742759 300
500 -899.28626 -922.45519 23.168929 233.69313
1000 -899.29247 -925.86547 26.573002 268.02828
1500 -899.27957 -916.95478 17.675214 178.28084
2000 -899.28171 -918.38728 19.105573 192.70814
2500 -899.28732 -922.50423 23.21691 234.17709
3000 -899.28195 -918.74112 19.459174 196.27473
3500 -899.27944 -918.03105 18.751604 189.13784
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 5.84317 on 1 procs for 5000 steps with 768 atoms
Performance: 73.932 ns/day, 0.325 hours/ns, 855.700 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6796 | 5.6796 | 5.6796 | 0.0 | 97.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026354 | 0.026354 | 0.026354 | 0.0 | 0.45
Output | 0.0014959 | 0.0014959 | 0.0014959 | 0.0 | 0.03
Modify | 0.090437 | 0.090437 | 0.090437 | 0.0 | 1.55
Other | | 0.04524 | | | 0.77
Nlocal: 768.000 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 354.000 ave 354 max 354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 20480.0 ave 20480 max 20480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20480
Ave neighs/atom = 26.666667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

781
examples/threebody/single_layer_MoS2.data Normal file
View File

@ -0,0 +1,781 @@
Single layer MoS2
768 atoms
3 atom types
0.0000000000000000 51.1523200000000177 xlo xhi
0.0000000000000000 44.2992085825108320 ylo yhi
-100.0000000000000000 100.0000000000000000 zlo zhi
25.5761600000000088 0.0000000000000000 0.0000000000000000 xy xz yz
Atoms
1 2 0.000000000000000 0.000000000000000 -1.596930000000000
2 3 0.000000000000000 0.000000000000000 1.596930000000000
3 1 0.000000000000000 1.845800357604618 0.000000000000000
4 2 1.598510000000001 2.768700536406927 -1.596930000000000
5 3 1.598510000000001 2.768700536406927 1.596930000000000
6 1 1.598510000000001 4.614500894011545 0.000000000000000
7 2 3.197020000000001 5.537401072813854 -1.596930000000000
8 3 3.197020000000001 5.537401072813854 1.596930000000000
9 1 3.197020000000001 7.383201430418472 0.000000000000000
10 2 4.795530000000002 8.306101609220781 -1.596930000000000
11 3 4.795530000000002 8.306101609220781 1.596930000000000
12 1 4.795530000000002 10.151901966825399 0.000000000000000
13 2 6.394040000000002 11.074802145627708 -1.596930000000000
14 3 6.394040000000002 11.074802145627708 1.596930000000000
15 1 6.394040000000002 12.920602503232326 0.000000000000000
16 2 7.992550000000003 13.843502682034635 -1.596930000000000
17 3 7.992550000000003 13.843502682034635 1.596930000000000
18 1 7.992550000000003 15.689303039639253 0.000000000000000
19 2 9.591060000000003 16.612203218441562 -1.596930000000000
20 3 9.591060000000003 16.612203218441562 1.596930000000000
21 1 9.591060000000003 18.458003576046180 0.000000000000000
22 2 11.189570000000004 19.380903754848489 -1.596930000000000
23 3 11.189570000000004 19.380903754848489 1.596930000000000
24 1 11.189570000000004 21.226704112453107 0.000000000000000
25 2 12.788080000000004 22.149604291255416 -1.596930000000000
26 3 12.788080000000004 22.149604291255416 1.596930000000000
27 1 12.788080000000004 23.995404648860034 0.000000000000000
28 2 14.386590000000005 24.918304827662343 -1.596930000000000
29 3 14.386590000000005 24.918304827662343 1.596930000000000
30 1 14.386590000000005 26.764105185266961 0.000000000000000
31 2 15.985100000000006 27.687005364069270 -1.596930000000000
32 3 15.985100000000006 27.687005364069270 1.596930000000000
33 1 15.985100000000006 29.532805721673888 0.000000000000000
34 2 17.583610000000006 30.455705900476197 -1.596930000000000
35 3 17.583610000000006 30.455705900476197 1.596930000000000
36 1 17.583610000000006 32.301506258080815 0.000000000000000
37 2 19.182120000000007 33.224406436883124 -1.596930000000000
38 3 19.182120000000007 33.224406436883124 1.596930000000000
39 1 19.182120000000007 35.070206794487742 0.000000000000000
40 2 20.780630000000007 35.993106973290051 -1.596930000000000
41 3 20.780630000000007 35.993106973290051 1.596930000000000
42 1 20.780630000000007 37.838907330894669 0.000000000000000
43 2 22.379140000000008 38.761807509696978 -1.596930000000000
44 3 22.379140000000008 38.761807509696978 1.596930000000000
45 1 22.379140000000008 40.607607867301596 0.000000000000000
46 2 23.977650000000008 41.530508046103905 -1.596930000000000
47 3 23.977650000000008 41.530508046103905 1.596930000000000
48 1 23.977650000000008 43.376308403708523 0.000000000000000
49 2 3.197020000000001 0.000000000000000 -1.596930000000000
50 3 3.197020000000001 0.000000000000000 1.596930000000000
51 1 3.197020000000001 1.845800357604618 0.000000000000000
52 2 4.795530000000002 2.768700536406927 -1.596930000000000
53 3 4.795530000000002 2.768700536406927 1.596930000000000
54 1 4.795530000000002 4.614500894011545 0.000000000000000
55 2 6.394040000000002 5.537401072813854 -1.596930000000000
56 3 6.394040000000002 5.537401072813854 1.596930000000000
57 1 6.394040000000002 7.383201430418472 0.000000000000000
58 2 7.992550000000003 8.306101609220781 -1.596930000000000
59 3 7.992550000000003 8.306101609220781 1.596930000000000
60 1 7.992550000000003 10.151901966825399 0.000000000000000
61 2 9.591060000000003 11.074802145627708 -1.596930000000000
62 3 9.591060000000003 11.074802145627708 1.596930000000000
63 1 9.591060000000003 12.920602503232326 0.000000000000000
64 2 11.189570000000004 13.843502682034635 -1.596930000000000
65 3 11.189570000000004 13.843502682034635 1.596930000000000
66 1 11.189570000000004 15.689303039639253 0.000000000000000
67 2 12.788080000000004 16.612203218441562 -1.596930000000000
68 3 12.788080000000004 16.612203218441562 1.596930000000000
69 1 12.788080000000004 18.458003576046180 0.000000000000000
70 2 14.386590000000005 19.380903754848489 -1.596930000000000
71 3 14.386590000000005 19.380903754848489 1.596930000000000
72 1 14.386590000000005 21.226704112453107 0.000000000000000
73 2 15.985100000000006 22.149604291255416 -1.596930000000000
74 3 15.985100000000006 22.149604291255416 1.596930000000000
75 1 15.985100000000006 23.995404648860034 0.000000000000000
76 2 17.583610000000006 24.918304827662343 -1.596930000000000
77 3 17.583610000000006 24.918304827662343 1.596930000000000
78 1 17.583610000000006 26.764105185266961 0.000000000000000
79 2 19.182120000000007 27.687005364069270 -1.596930000000000
80 3 19.182120000000007 27.687005364069270 1.596930000000000
81 1 19.182120000000007 29.532805721673888 0.000000000000000
82 2 20.780630000000007 30.455705900476197 -1.596930000000000
83 3 20.780630000000007 30.455705900476197 1.596930000000000
84 1 20.780630000000007 32.301506258080815 0.000000000000000
85 2 22.379140000000008 33.224406436883124 -1.596930000000000
86 3 22.379140000000008 33.224406436883124 1.596930000000000
87 1 22.379140000000008 35.070206794487742 0.000000000000000
88 2 23.977650000000008 35.993106973290051 -1.596930000000000
89 3 23.977650000000008 35.993106973290051 1.596930000000000
90 1 23.977650000000008 37.838907330894669 0.000000000000000
91 2 25.576160000000009 38.761807509696978 -1.596930000000000
92 3 25.576160000000009 38.761807509696978 1.596930000000000
93 1 25.576160000000009 40.607607867301596 0.000000000000000
94 2 27.174670000000009 41.530508046103905 -1.596930000000000
95 3 27.174670000000009 41.530508046103905 1.596930000000000
96 1 27.174670000000009 43.376308403708523 0.000000000000000
97 2 6.394040000000002 0.000000000000000 -1.596930000000000
98 3 6.394040000000002 0.000000000000000 1.596930000000000
99 1 6.394040000000002 1.845800357604618 0.000000000000000
100 2 7.992550000000003 2.768700536406927 -1.596930000000000
101 3 7.992550000000003 2.768700536406927 1.596930000000000
102 1 7.992550000000003 4.614500894011545 0.000000000000000
103 2 9.591060000000003 5.537401072813854 -1.596930000000000
104 3 9.591060000000003 5.537401072813854 1.596930000000000
105 1 9.591060000000003 7.383201430418472 0.000000000000000
106 2 11.189570000000004 8.306101609220781 -1.596930000000000
107 3 11.189570000000004 8.306101609220781 1.596930000000000
108 1 11.189570000000004 10.151901966825399 0.000000000000000
109 2 12.788080000000004 11.074802145627708 -1.596930000000000
110 3 12.788080000000004 11.074802145627708 1.596930000000000
111 1 12.788080000000004 12.920602503232326 0.000000000000000
112 2 14.386590000000005 13.843502682034635 -1.596930000000000
113 3 14.386590000000005 13.843502682034635 1.596930000000000
114 1 14.386590000000005 15.689303039639253 0.000000000000000
115 2 15.985100000000006 16.612203218441562 -1.596930000000000
116 3 15.985100000000006 16.612203218441562 1.596930000000000
117 1 15.985100000000006 18.458003576046180 0.000000000000000
118 2 17.583610000000006 19.380903754848489 -1.596930000000000
119 3 17.583610000000006 19.380903754848489 1.596930000000000
120 1 17.583610000000006 21.226704112453107 0.000000000000000
121 2 19.182120000000007 22.149604291255416 -1.596930000000000
122 3 19.182120000000007 22.149604291255416 1.596930000000000
123 1 19.182120000000007 23.995404648860034 0.000000000000000
124 2 20.780630000000007 24.918304827662343 -1.596930000000000
125 3 20.780630000000007 24.918304827662343 1.596930000000000
126 1 20.780630000000007 26.764105185266961 0.000000000000000
127 2 22.379140000000008 27.687005364069270 -1.596930000000000
128 3 22.379140000000008 27.687005364069270 1.596930000000000
129 1 22.379140000000008 29.532805721673888 0.000000000000000
130 2 23.977650000000008 30.455705900476197 -1.596930000000000
131 3 23.977650000000008 30.455705900476197 1.596930000000000
132 1 23.977650000000008 32.301506258080815 0.000000000000000
133 2 25.576160000000009 33.224406436883124 -1.596930000000000
134 3 25.576160000000009 33.224406436883124 1.596930000000000
135 1 25.576160000000009 35.070206794487742 0.000000000000000
136 2 27.174670000000009 35.993106973290051 -1.596930000000000
137 3 27.174670000000009 35.993106973290051 1.596930000000000
138 1 27.174670000000009 37.838907330894669 0.000000000000000
139 2 28.773180000000010 38.761807509696978 -1.596930000000000
140 3 28.773180000000010 38.761807509696978 1.596930000000000
141 1 28.773180000000010 40.607607867301596 0.000000000000000
142 2 30.371690000000011 41.530508046103905 -1.596930000000000
143 3 30.371690000000011 41.530508046103905 1.596930000000000
144 1 30.371690000000011 43.376308403708523 0.000000000000000
145 2 9.591060000000003 0.000000000000000 -1.596930000000000
146 3 9.591060000000003 0.000000000000000 1.596930000000000
147 1 9.591060000000003 1.845800357604618 0.000000000000000
148 2 11.189570000000004 2.768700536406927 -1.596930000000000
149 3 11.189570000000004 2.768700536406927 1.596930000000000
150 1 11.189570000000004 4.614500894011545 0.000000000000000
151 2 12.788080000000004 5.537401072813854 -1.596930000000000
152 3 12.788080000000004 5.537401072813854 1.596930000000000
153 1 12.788080000000004 7.383201430418472 0.000000000000000
154 2 14.386590000000005 8.306101609220781 -1.596930000000000
155 3 14.386590000000005 8.306101609220781 1.596930000000000
156 1 14.386590000000005 10.151901966825399 0.000000000000000
157 2 15.985100000000006 11.074802145627708 -1.596930000000000
158 3 15.985100000000006 11.074802145627708 1.596930000000000
159 1 15.985100000000006 12.920602503232326 0.000000000000000
160 2 17.583610000000006 13.843502682034635 -1.596930000000000
161 3 17.583610000000006 13.843502682034635 1.596930000000000
162 1 17.583610000000006 15.689303039639253 0.000000000000000
163 2 19.182120000000007 16.612203218441562 -1.596930000000000
164 3 19.182120000000007 16.612203218441562 1.596930000000000
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1
examples/threebody/tmd.sw.mod Symbolic link
View File

@ -0,0 +1 @@
../../potentials/tmd.sw.mod

2
lib/gpu/Makefile.cuda_mps
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA with the Multi-Process Service (MPS)
# - change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.hip
View File

@ -39,11 +39,9 @@ HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
ifeq (hcc,$(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))

10
lib/gpu/Makefile.linux
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -13,7 +13,7 @@ endif
NVCC = nvcc
# obsolete hardware. not supported by current drivers anymore.
# obsolete hardware. not supported by current drivers and toolkits anymore.
#CUDA_ARCH = -arch=sm_13
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
@ -28,11 +28,11 @@ NVCC = nvcc
#CUDA_ARCH = -arch=sm_37
# Maxwell hardware
CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_52
# Pascal hardware
#CUDA_ARCH = -arch=sm_60
CUDA_ARCH = -arch=sm_60
#CUDA_ARCH = -arch=sm_61
# Volta hardware
@ -70,7 +70,7 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
# GPU binning not recommended with modern GPUs
# GPU binning not recommended for most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

4
lib/gpu/Makefile.linux_multi
View File

@ -1,6 +1,6 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# Generic Linux Makefile for CUDA complied for multiple compute capabilities
# - Add your GPU to CUDA_CODE
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps

1
lib/gpu/Makefile.mpi Symbolic link
View File

@ -0,0 +1 @@
Makefile.linux

10
lib/gpu/Makefile.serial
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA without MPI libraries
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -28,11 +28,11 @@ NVCC = nvcc
#CUDA_ARCH = -arch=sm_37
# Maxwell hardware
CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_52
# Pascal hardware
#CUDA_ARCH = -arch=sm_60
CUDA_ARCH = -arch=sm_60
#CUDA_ARCH = -arch=sm_61
# Volta hardware
@ -41,6 +41,10 @@ CUDA_ARCH = -arch=sm_50
# Turing hardware
#CUDA_ARCH = -arch=sm_75
# Ampere hardware
#CUDA_ARCH = -arch=sm_80
#CUDA_ARCH = -arch=sm_86
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL

23
lib/gpu/Makefile.turing
View File

@ -1,23 +0,0 @@
NVCC = $(CUDA_HOME)/bin/nvcc
EXTRAMAKE = Makefile.lammps.standard
CUDA_ARCH = -arch=sm_75
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON -DLAMMPS_SMALLBIG
BIN_DIR = .
OBJ_DIR = obj
LIB_DIR = .
AR = ar
BSH = /bin/sh
# GPU binning not recommended with most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

4
lib/kim/Install.py
View File

@ -17,6 +17,8 @@ parser = ArgumentParser(prog='Install.py',
# settings
CMAKE = os.environ.get('CMAKE') or 'cmake'
thisdir = fullpath('.')
version = "2.2.1"
@ -141,7 +143,7 @@ if buildflag:
# configure kim-api
print("Configuring kim-api ...")
cmd = 'cd "%s/kim-api-%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
cmd = 'cd "%s/kim-api-%s" && mkdir build && cd build && %s .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,CMAKE,kimdir)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))

160
lib/kokkos/CHANGELOG.md
View File

@ -1,5 +1,165 @@
# Change Log
## [3.5.00](https://github.com/kokkos/kokkos/tree/3.5.00) (2021-10-19)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.4.01...3.5.00)
### Features:
- Add support for quad-precision math functions/traits [\#4098](https://github.com/kokkos/kokkos/pull/4098)
- Adding ExecutionSpace partitioning function [\#4096](https://github.com/kokkos/kokkos/pull/4096)
- Improve Python Interop Capabilities [\#4065](https://github.com/kokkos/kokkos/pull/4065)
- Add half_t Kokkos::rand specialization [\#3922](https://github.com/kokkos/kokkos/pull/3922)
- Add math special functions: erf, erfcx, expint1, Bessel functions, Hankel functions [\#3920](https://github.com/kokkos/kokkos/pull/3920)
- Add missing common mathematical functions [\#4043](https://github.com/kokkos/kokkos/pull/4043) [\#4036](https://github.com/kokkos/kokkos/pull/4036) [\#4034](https://github.com/kokkos/kokkos/pull/4034)
- Let the numeric traits be SFINAE-friendly [\#4038](https://github.com/kokkos/kokkos/pull/4038)
- Add Desul atomics - enabling memory-order and memory-scope parameters [\#3247](https://github.com/kokkos/kokkos/pull/3247)
- Add detection idiom from the C++ standard library extension version 2 [\#3980](https://github.com/kokkos/kokkos/pull/3980)
- Fence Profiling Support in all backends [\#3966](https://github.com/kokkos/kokkos/pull/3966) [\#4304](https://github.com/kokkos/kokkos/pull/4304) [\#4258](https://github.com/kokkos/kokkos/pull/4258) [\#4232](https://github.com/kokkos/kokkos/pull/4232)
- Significant SYCL enhancements (see below)
### Deprecations:
- Deprecate CUDA_SAFE_CALL and HIP_SAFE_CALL [\#4249](https://github.com/kokkos/kokkos/pull/4249)
- Deprecate Kokkos::Impl::Timer (Kokkos::Timer has been available for a long time) [\#4201](https://github.com/kokkos/kokkos/pull/4201)
- Deprecate Experimental::MasterLock [\#4094](https://github.com/kokkos/kokkos/pull/4094)
- Deprecate Kokkos_TaskPolicy.hpp (headers got reorganized, doesn't remove functionality) [\#4011](https://github.com/kokkos/kokkos/pull/4011)
- Deprecate backward compatibility features [\#3978](https://github.com/kokkos/kokkos/pull/3978)
- Update and deprecate is_space::host_memory/execution/mirror_space [\#3973](https://github.com/kokkos/kokkos/pull/3973)
### Backends and Archs Enhancements:
- Enabling constbitset constructors in kernels [\#4296](https://github.com/kokkos/kokkos/pull/4296)
- Use ZeroMemset in View constructor to improve performance [\#4226](https://github.com/kokkos/kokkos/pull/4226)
- Use memset in deep_copy [\#3944](https://github.com/kokkos/kokkos/pull/3944)
- Add missing fence() calls in resize(View) that effectively do deep_copy(resized, orig) [\#4212](https://github.com/kokkos/kokkos/pull/4212)
- Avoid allocations in resize and realloc [\#4207](https://github.com/kokkos/kokkos/pull/4207)
- StaticCsrGraph: use device type instead of execution space to construct views [\#3991](https://github.com/kokkos/kokkos/pull/3991)
- Consider std::sort when view is accessible from host [\#3929](https://github.com/kokkos/kokkos/pull/3929)
- Fix CPP20 warnings except for volatile [\#4312](https://github.com/kokkos/kokkos/pull/4312)
#### SYCL:
- Introduce SYCLHostUSMSpace [\#4268](https://github.com/kokkos/kokkos/pull/4268)
- Implement SYCL TeamPolicy for vector_size > 1 [\#4183](https://github.com/kokkos/kokkos/pull/4183)
- Enable 64bit ranges for SYCL [\#4211](https://github.com/kokkos/kokkos/pull/4211)
- Don't print SYCL device info in execution space intialization [\#4168](https://github.com/kokkos/kokkos/pull/4168)
- Improve SYCL MDRangePolicy performance [\#4161](https://github.com/kokkos/kokkos/pull/4161)
- Use sub_groups in SYCL parallel_scan [\#4147](https://github.com/kokkos/kokkos/pull/4147)
- Implement subgroup reduction for SYCL RangePolicy parallel_reduce [\#3940](https://github.com/kokkos/kokkos/pull/3940)
- Use DPC++ broadcast extension in SYCL team_broadcast [\#4103](https://github.com/kokkos/kokkos/pull/4103)
- Only fence in SYCL parallel_reduce for non-device-accessible result_ptr [\#4089](https://github.com/kokkos/kokkos/pull/4089)
- Improve fencing behavior in SYCL backend [\#4088](https://github.com/kokkos/kokkos/pull/4088)
- Fence all registered SYCL queues before deallocating memory [\#4086](https://github.com/kokkos/kokkos/pull/4086)
- Implement SYCL::print_configuration [\#3992](https://github.com/kokkos/kokkos/pull/3992)
- Reuse scratch memory in parallel_scan and TeamPolicy (decreases memory footprint) [\#3899](https://github.com/kokkos/kokkos/pull/3899) [\#3889](https://github.com/kokkos/kokkos/pull/3889)
#### CUDA:
- Cuda improve heuristic for blocksize [\#4271](https://github.com/kokkos/kokkos/pull/4271)
- Don't use [[deprecated]] for nvcc [\#4229](https://github.com/kokkos/kokkos/pull/4229)
- Improve error message for NVHPC as host compiler [\#4227](https://github.com/kokkos/kokkos/pull/4227)
- Update support for cuda reductions to work with types < 4bytes [\#4156](https://github.com/kokkos/kokkos/pull/4156)
- Fix incompatible team size deduction in rare cases parallel_reduce [\#4142](https://github.com/kokkos/kokkos/pull/4142)
- Remove UVM usage in DynamicView [\#4129](https://github.com/kokkos/kokkos/pull/4129)
- Remove dependency between core and containers [\#4114](https://github.com/kokkos/kokkos/pull/4114)
- Adding opt-in CudaMallocSync support when using CUDA version >= 11.2 [\#4026](https://github.com/kokkos/kokkos/pull/4026) [\#4233](https://github.com/kokkos/kokkos/pull/4233)
- Fix a potential race condition in the CUDA backend [\#3999](https://github.com/kokkos/kokkos/pull/3999)
#### HIP:
- Implement new blocksize deduction method for HIP Backend [\#3953](https://github.com/kokkos/kokkos/pull/3953)
- Add multiple LaunchMechanism [\#3820](https://github.com/kokkos/kokkos/pull/3820)
- Make HIP backend thread-safe [\#4170](https://github.com/kokkos/kokkos/pull/4170)
#### Serial:
- Refactor Serial backend and fix thread-safety issue [\#4053](https://github.com/kokkos/kokkos/pull/4053)
#### OpenMPTarget:
- OpenMPTarget: support array reductions in RangePolicy [\#4040](https://github.com/kokkos/kokkos/pull/4040)
- OpenMPTarget: add MDRange parallel_reduce [\#4032](https://github.com/kokkos/kokkos/pull/4032)
- OpenMPTarget: Fix bug in for the case of a reducer. [\#4044](https://github.com/kokkos/kokkos/pull/4044)
- OpenMPTarget: verify process fix [\#4041](https://github.com/kokkos/kokkos/pull/4041)
### Implemented enhancements BuildSystem
#### Important BuildSystem Updates:
- Use hipcc architecture autodetection when Kokkos_ARCH is not set [\#3941](https://github.com/kokkos/kokkos/pull/3941)
- Introduce Kokkos_ENABLE_DEPRECATION_WARNINGS and remove deprecated code with Kokkos_ENABLE_DEPRECATED_CODE_3 [\#4106](https://github.com/kokkos/kokkos/pull/4106) [\#3855](https://github.com/kokkos/kokkos/pull/3855)
#### Other Improvements:
- Add allow-unsupported-compiler flag to nvcc-wrapper [\#4298](https://github.com/kokkos/kokkos/pull/4298)
- nvcc_wrapper: fix errors in argument handling [\#3993](https://github.com/kokkos/kokkos/pull/3993)
- Adds support for -time=<file> and -time <file> in nvcc_wrapper [\#4015](https://github.com/kokkos/kokkos/pull/4015)
- nvcc_wrapper: suppress duplicates of GPU architecture and RDC flags [\#3968](https://github.com/kokkos/kokkos/pull/3968)
- Fix TMPDIR support in nvcc_wrapper [\#3792](https://github.com/kokkos/kokkos/pull/3792)
- NVHPC: update PGI compiler arch flags [\#4133](https://github.com/kokkos/kokkos/pull/4133)
- Replace PGI with NVHPC (works for both) [\#4196](https://github.com/kokkos/kokkos/pull/4196)
- Make sure that KOKKOS_CXX_HOST_COMPILER_ID is defined [\#4235](https://github.com/kokkos/kokkos/pull/4235)
- Add options to Makefile builds for deprecated code and warnings [\#4215](https://github.com/kokkos/kokkos/pull/4215)
- Use KOKKOS_CXX_HOST_COMPILER_ID for identifying CPU arch flags [\#4199](https://github.com/kokkos/kokkos/pull/4199)
- Added support for Cray Clang to Makefile.kokkos [\#4176](https://github.com/kokkos/kokkos/pull/4176)
- Add XLClang as compiler [\#4120](https://github.com/kokkos/kokkos/pull/4120)
- Keep quoted compiler flags when passing to Trilinos [\#3987](https://github.com/kokkos/kokkos/pull/3987)
- Add support for AMD Zen3 CPU architecture [\#3972](https://github.com/kokkos/kokkos/pull/3972)
- Rename IntelClang to IntelLLVM [\#3945](https://github.com/kokkos/kokkos/pull/3945)
- Add cppcoreguidelines-pro-type-cstyle-cast to clang-tidy [\#3522](https://github.com/kokkos/kokkos/pull/3522)
- Add sve bit size definition for A64FX [\#3947](https://github.com/kokkos/kokkos/pull/3947) [\#3946](https://github.com/kokkos/kokkos/pull/3946)
- Remove KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES [\#4150](https://github.com/kokkos/kokkos/pull/4150)
### Other Changes:
#### Tool Enhancements:
- Retrieve original value from a point in a MultidimensionalSparseTuningProblem [\#3977](https://github.com/kokkos/kokkos/pull/3977)
- Allow extension of built-in tuners with additional tuning axes [\#3961](https://github.com/kokkos/kokkos/pull/3961)
- Added a categorical tuner [\#3955](https://github.com/kokkos/kokkos/pull/3955)
#### Miscellaneous:
- hpcbind: Use double quotes around $@ when invoking user command [\#4284](https://github.com/kokkos/kokkos/pull/4284)
- Add file and line to error message [\#3985](https://github.com/kokkos/kokkos/pull/3985)
- Fix compiler warnings when compiling with nvc++ [\#4198](https://github.com/kokkos/kokkos/pull/4198)
- Add OpenMPTarget CI build on AMD GPUs [\#4055](https://github.com/kokkos/kokkos/pull/4055)
- CI: icpx is now part of intel container [\#4002](https://github.com/kokkos/kokkos/pull/4002)
### Incompatibilities:
- Remove pre CUDA 9 KOKKOS_IMPL_CUDA_* macros [\#4138](https://github.com/kokkos/kokkos/pull/4138)
### Bug Fixes:
- UnorderedMap::clear() should zero the size() [\#4130](https://github.com/kokkos/kokkos/pull/4130)
- Add memory fence for HostSharedPtr::cleanup() [\#4144](https://github.com/kokkos/kokkos/pull/4144)
- SYCL: Fix race conditions in TeamPolicy::parallel_reduce [\#4418](https://github.com/kokkos/kokkos/pull/4418)
- Adding missing memory fence to serial exec space fence. [\#4292](https://github.com/kokkos/kokkos/pull/4292)
- Fix using external SYCL queues in tests [\#4291](https://github.com/kokkos/kokkos/pull/4291)
- Fix digits10 bug [\#4281](https://github.com/kokkos/kokkos/pull/4281)
- Fixes constexpr errors with frounding-math on gcc < 10. [\#4278](https://github.com/kokkos/kokkos/pull/4278)
- Fix compiler flags for PGI/NVHPC [\#4264](https://github.com/kokkos/kokkos/pull/4264)
- Fix Zen2/3 also implying Zen Arch with Makefiles [\#4260](https://github.com/kokkos/kokkos/pull/4260)
- Kokkos_Cuda.hpp: Fix shadow warning with cuda/11.0 [\#4252](https://github.com/kokkos/kokkos/pull/4252)
- Fix issue w/ static initialization of function attributes [\#4242](https://github.com/kokkos/kokkos/pull/4242)
- Disable long double hypot test on Power systems [\#4221](https://github.com/kokkos/kokkos/pull/4221)
- Fix false sharing in random pool [\#4218](https://github.com/kokkos/kokkos/pull/4218)
- Fix a missing memory_fence for debug shared alloc code [\#4216](https://github.com/kokkos/kokkos/pull/4216)
- Fix two xl issues [\#4179](https://github.com/kokkos/kokkos/pull/4179)
- Makefile.kokkos: fix (standard_in) 1: syntax error [\#4173](https://github.com/kokkos/kokkos/pull/4173)
- Fixes for query_device example [\#4172](https://github.com/kokkos/kokkos/pull/4172)
- Fix a bug when using HIP atomic with Kokkos::Complex [\#4159](https://github.com/kokkos/kokkos/pull/4159)
- Fix mistaken logic in pthread creation [\#4157](https://github.com/kokkos/kokkos/pull/4157)
- Define KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION when requesting Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON [\#4107](https://github.com/kokkos/kokkos/pull/4107)
- Fix compilation with latest MSVC version [\#4102](https://github.com/kokkos/kokkos/pull/4102)
- Fix incorrect macro definitions when compiling with Intel compiler on Windows [\#4087](https://github.com/kokkos/kokkos/pull/4087)
- Fixup global buffer overflow in hand rolled string manipulation [\#4070](https://github.com/kokkos/kokkos/pull/4070)
- Fixup heap buffer overflow in cmd line args parsing unit tests [\#4069](https://github.com/kokkos/kokkos/pull/4069)
- Only add quotes in compiler flags for Trilinos if necessary [\#4067](https://github.com/kokkos/kokkos/pull/4067)
- Fixed invocation of tools init callbacks [\#4061](https://github.com/kokkos/kokkos/pull/4061)
- Work around SYCL JIT compiler issues with static variables [\#4013](https://github.com/kokkos/kokkos/pull/4013)
- Fix TestDetectionIdiom.cpp test inclusion for Trilinos/TriBITS [\#4010](https://github.com/kokkos/kokkos/pull/4010)
- Fixup allocation headers with OpenMPTarget backend [\#4003](https://github.com/kokkos/kokkos/pull/4003)
- Add missing specialization for OMPT to Kokkos Random [\#3967](https://github.com/kokkos/kokkos/pull/3967)
- Disable hypot long double test on power arches [\#3962](https://github.com/kokkos/kokkos/pull/3962)
- Use different EBO workaround for MSVC (rebased) [\#3924](https://github.com/kokkos/kokkos/pull/3924)
- Fix SYCL Kokkos::Profiling::(de)allocateData calls [\#3928](https://github.com/kokkos/kokkos/pull/3928)
## [3.4.01](https://github.com/kokkos/kokkos/tree/3.4.01) (2021-05-19)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.4.00...3.4.01)

11
lib/kokkos/CMakeLists.txt
View File

@ -111,8 +111,8 @@ ENDIF()
set(Kokkos_VERSION_MAJOR 3)
set(Kokkos_VERSION_MINOR 4)
set(Kokkos_VERSION_PATCH 01)
set(Kokkos_VERSION_MINOR 5)
set(Kokkos_VERSION_PATCH 00)
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
@ -210,7 +210,12 @@ IF (KOKKOS_HAS_TRILINOS)
# which needs another workaround.
SET(KOKKOS_COMPILE_OPTIONS_TMP)
FOREACH(OPTION ${KOKKOS_COMPILE_OPTIONS})
LIST(APPEND KOKKOS_COMPILE_OPTIONS_TMP \"${OPTION}\")
STRING(FIND "${OPTION}" " " OPTION_HAS_WHITESPACE)
IF(OPTION_HAS_WHITESPACE EQUAL -1)
LIST(APPEND KOKKOS_COMPILE_OPTIONS_TMP "${OPTION}")
ELSE()
LIST(APPEND KOKKOS_COMPILE_OPTIONS_TMP "\"${OPTION}\"")
ENDIF()
ENDFOREACH()
STRING(REPLACE ";" " " KOKKOSCORE_COMPILE_OPTIONS "${KOKKOS_COMPILE_OPTIONS_TMP}")
LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS ${KOKKOS_COMPILE_OPTIONS})

242
lib/kokkos/Makefile.kokkos
View File

@ -11,20 +11,21 @@ CXXFLAGS += $(SHFLAGS)
endif
KOKKOS_VERSION_MAJOR = 3
KOKKOS_VERSION_MINOR = 4
KOKKOS_VERSION_PATCH = 01
KOKKOS_VERSION_MINOR = 5
KOKKOS_VERSION_PATCH = 00
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
# Options: Cuda,HIP,OpenMP,Pthread,Serial
# Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Pthread,Serial
KOKKOS_DEVICES ?= "OpenMP"
#KOKKOS_DEVICES ?= "Pthread"
# Options:
# Options:
# Intel: KNC,KNL,SNB,HSW,BDW,SKX
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX
# IBM: BGQ,Power7,Power8,Power9
# AMD-GPUS: Vega900,Vega906,Vega908
# AMD-GPUS: Vega900,Vega906,Vega908,Vega90A
# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3
# Intel-GPUs: Gen9,Gen11,Gen12LP,DG1,XeHP
KOKKOS_ARCH ?= ""
# Options: yes,no
KOKKOS_DEBUG ?= "no"
@ -32,8 +33,8 @@ KOKKOS_DEBUG ?= "no"
KOKKOS_USE_TPLS ?= ""
# Options: c++14,c++1y,c++17,c++1z,c++2a
KOKKOS_CXX_STANDARD ?= "c++14"
# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align
KOKKOS_OPTIONS ?= ""
# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align,disable_deprecated_code,enable_deprecation_warnings,enable_desul_atomics
KOKKOS_OPTIONS ?= "enable_desul_atomics"
KOKKOS_CMAKE ?= "no"
KOKKOS_TRIBITS ?= "no"
KOKKOS_STANDALONE_CMAKE ?= "no"
@ -80,7 +81,7 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),exper
# Check for advanced settings.
KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings)
KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization)
KOKKOS_INTERNAL_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization)
KOKKOS_INTERNAL_ENABLE_TUNING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_tuning)
KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_complex_align)
KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check)
@ -92,6 +93,9 @@ KOKKOS_INTERNAL_CUDA_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS
KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda)
KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_constexpr)
KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH := $(call kokkos_has_string,$(KOKKOS_HPX_OPTIONS),enable_async_dispatch)
KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_desul_atomics)
KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_deprecated_code)
KOKKOS_INTERNAL_ENABLE_DEPRECATION_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_deprecation_warnings)
KOKKOS_INTERNAL_HIP_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_HIP_OPTIONS),rdc)
@ -112,6 +116,7 @@ endif
# Check for other Execution Spaces.
KOKKOS_INTERNAL_USE_CUDA := $(call kokkos_has_string,$(KOKKOS_DEVICES),Cuda)
KOKKOS_INTERNAL_USE_HIP := $(call kokkos_has_string,$(KOKKOS_DEVICES),HIP)
KOKKOS_INTERNAL_USE_SYCL := $(call kokkos_has_string,$(KOKKOS_DEVICES),SYCL)
KOKKOS_INTERNAL_USE_OPENMPTARGET := $(call kokkos_has_string,$(KOKKOS_DEVICES),OpenMPTarget)
KOKKOS_DEVICELIST =
@ -133,11 +138,18 @@ endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
KOKKOS_DEVICELIST += HIP
endif
KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER := $(shell expr $(KOKKOS_INTERNAL_ENABLE_CXX17) \
+ $(KOKKOS_INTERNAL_ENABLE_CXX20) \
+ $(KOKKOS_INTERNAL_ENABLE_CXX2A))
ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
KOKKOS_DEVICELIST += SYCL
ifneq ($(KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER), 1)
$(error SYCL backend requires C++17 or newer)
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
KOKKOS_DEVICELIST += OPENMPTARGET
KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER := $(shell expr $(KOKKOS_INTERNAL_ENABLE_CXX17) \
+ $(KOKKOS_INTERNAL_ENABLE_CXX20) \
+ $(KOKKOS_INTERNAL_ENABLE_CXX2A))
ifneq ($(KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER), 1)
$(error OpenMPTarget backend requires C++17 or newer)
endif
@ -168,6 +180,8 @@ KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2
KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "CC-"))
KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell echo "$(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version 2>&1 | grep -c nvcc)>0" | bc))
KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang)
KOKKOS_INTERNAL_COMPILER_CRAY_CLANG := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep -c "clang++"))
KOKKOS_INTERNAL_COMPILER_INTEL_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),oneAPI)
KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Apple clang)
KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC)
KOKKOS_INTERNAL_COMPILER_GCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),GCC)
@ -247,7 +261,11 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
KOKKOS_INTERNAL_OPENMP_FLAG := -mp
else
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY_CLANG), 1)
KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp
else
KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp
endif
else
ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1)
KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp
@ -259,7 +277,11 @@ else
# OpenMP is turned on by default in Cray compiler environment.
KOKKOS_INTERNAL_OPENMP_FLAG :=
else
KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL_CLANG), 1)
KOKKOS_INTERNAL_OPENMP_FLAG := -fiopenmp
else
KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp
endif
endif
endif
endif
@ -317,6 +339,13 @@ KOKKOS_INTERNAL_USE_ARCH_BDW := $(call kokkos_has_string,$(KOKKOS_ARCH),BDW)
KOKKOS_INTERNAL_USE_ARCH_SKX := $(call kokkos_has_string,$(KOKKOS_ARCH),SKX)
KOKKOS_INTERNAL_USE_ARCH_KNL := $(call kokkos_has_string,$(KOKKOS_ARCH),KNL)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen9)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen11)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen12LP)
KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelDG1)
KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelXeHP)
# NVIDIA based.
NVCC_WRAPPER := $(KOKKOS_PATH)/bin/nvcc_wrapper
KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler30)
@ -384,20 +413,25 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_
KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX)
KOKKOS_INTERNAL_USE_ARCH_ZEN3 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen3)
KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2)
KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN3), 0)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 0)
KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen)
endif
endif
KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
KOKKOS_INTERNAL_USE_ARCH_VEGA908 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega908)
KOKKOS_INTERNAL_USE_ARCH_VEGA90A := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega90A)
# Any AVX?
KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3))
KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3))
KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL))
KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX))
# Decide what ISA level we are able to support.
KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2)) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3))
KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN3))
KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC))
KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9))
KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7))
@ -406,7 +440,7 @@ KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POW
KOKKOS_INTERNAL_USE_TM := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_SKX))
# Incompatible flags?
KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1") | bc )
KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1") | bc)
KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1") | bc)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MULTIHOST), 1)
@ -442,6 +476,10 @@ KOKKOS_LINK_FLAGS =
KOKKOS_SRC =
KOKKOS_HEADERS =
#ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1)
KOKKOS_LIBS += -latomic
#endif
# Generating the KokkosCore_config.h file.
KOKKOS_INTERNAL_CONFIG_TMP=KokkosCore_config.tmp
@ -478,6 +516,10 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_HIP')
endif
ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_SYCL')
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_OPENMPTARGET')
ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1)
@ -533,6 +575,12 @@ endif
#only add the c++ standard flags if this is not CMake
tmp := $(call kokkos_append_header,"/* General Settings */")
ifneq ($(KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEPRECATED_CODE_3")
endif
ifeq ($(KOKKOS_INTERNAL_ENABLE_DEPRECATION_WARNINGS), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEPRECATION_WARNINGS")
endif
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1)
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG)
@ -635,8 +683,10 @@ endif
tmp := $(call kokkos_append_header,"/* Optimization Settings */")
ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1)
ifeq ($(KOKKOS_INTERNAL_AGGRESSIVE_VECTORIZATION), 1)
# deprecated
tmp := $(call kokkos_append_header,"$H""define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION")
endif
tmp := $(call kokkos_append_header,"/* Cuda Settings */")
@ -1166,6 +1216,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA908")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx908
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA90A), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 90A")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA90A")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx90a
endif
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp)
@ -1184,6 +1239,52 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
endif
endif
# Figure out the architecture flag for SYCL.
ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
# Lets start with adding architecture defines
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9-"
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN9")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen9"
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN11")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen11"
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GEN12LP")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device gen12lp"
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_DG1")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device dg1"
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_GPU")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_INTEL_XEHP")
KOKKOS_INTERNAL_SYCL_ARCH_FLAG := -fsycl-targets=spir64_gen-unknown-unknown-sycldevice -Xsycl-target-backend "-device xehp"
endif
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/SYCL/*.cpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/SYCL/*.hpp)
KOKKOS_CXXFLAGS+=-fsycl -fno-sycl-id-queries-fit-in-int -fsycl-unnamed-lambda
KOKKOS_CXXFLAGS+=$(KOKKOS_INTERNAL_SYCL_ARCH_FLAG)
KOKKOS_LDFLAGS+=-fsycl
KOKKOS_LDFLAGS+=$(KOKKOS_INTERNAL_SYCL_ARCH_FLAG)
endif
ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_IMPL_DESUL_ATOMICS")
endif
KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h 2>&1)
@ -1196,56 +1297,62 @@ endif
ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0)
tmp := $(shell cp KokkosCore_config.tmp KokkosCore_config.h)
# Functions for generating config header file
kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1)
kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3)
kokkos_append_config_header = $(shell echo $1 >> $2))
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp")
tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp")
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_CUDA.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_CUDA.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_Cuda.hpp>","KokkosCore_Config_SetupBackend.hpp")
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
else
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_OPENMPTARGET.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_OPENMPTARGET.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HIP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HIP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_HIP.hpp>","KokkosCore_Config_SetupBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_OPENMP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_OPENMP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_THREADS.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_THREADS.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HPX.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HPX.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_SERIAL.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_SERIAL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HBWSpace.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HBWSpace.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
# Functions for generating config header file
kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1)
kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3)
kokkos_append_config_header = $(shell echo $1 >> $2))
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp")
tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp")
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_CUDA.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_CUDA.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_Cuda.hpp>","KokkosCore_Config_SetupBackend.hpp")
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
else
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_OPENMPTARGET.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_OPENMPTARGET.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_SYCL.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_SYCL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_SYCL.hpp>","KokkosCore_Config_SetupBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HIP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HIP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_HIP.hpp>","KokkosCore_Config_SetupBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_OPENMP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_OPENMP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_THREADS.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_THREADS.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HPX.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HPX.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_SERIAL.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_SERIAL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HBWSpace.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_HBWSpace.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
endif
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/containers/src/*.hpp)
@ -1257,6 +1364,9 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp)
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp)
ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1)
KOKKOS_SRC += $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp
endif
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp)
ifneq ($(CUDA_PATH),)
KOKKOS_CPPLAGS += -I$(CUDA_PATH)/include

11
lib/kokkos/Makefile.targets
View File

@ -48,6 +48,17 @@ Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cu
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
Lock_Array_CUDA.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_CUDA.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
Kokkos_SYCL.o : $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL.cpp
Kokkos_SYCL_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Space.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Space.cpp
Kokkos_SYCL_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/SYCL/Kokkos_SYCL_Instance.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)

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