Merge branch 'develop' into remove-fix-latte
This commit is contained in:
Steve Plimpton
6
.github/CODEOWNERS
vendored
6
.github/CODEOWNERS
vendored
@ -150,12 +150,12 @@ tools/vim/* @hammondkd
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|||||||
unittest/* @akohlmey
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unittest/* @akohlmey
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||||||
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# cmake
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# cmake
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||||||
cmake/* @junghans @rbberger
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cmake/* @rbberger
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||||||
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
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cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
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||||||
cmake/Modules/MPI4WIN.cmake @akohlmey
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cmake/Modules/MPI4WIN.cmake @akohlmey
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||||||
cmake/Modules/OpenCLLoader.cmake @akohlmey
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cmake/Modules/OpenCLLoader.cmake @akohlmey
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||||||
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
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cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
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||||||
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
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cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
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||||||
cmake/presets/*.cmake @akohlmey
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cmake/presets/*.cmake @akohlmey
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||||||
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||||||
# python
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# python
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||||||
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|||||||
@ -538,7 +538,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
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separate_arguments(CMAKE_TUNE_FLAGS)
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separate_arguments(CMAKE_TUNE_FLAGS)
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||||||
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
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foreach(_FLAG ${CMAKE_TUNE_FLAGS})
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||||||
target_compile_options(lammps PRIVATE ${_FLAG})
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target_compile_options(lammps PRIVATE ${_FLAG})
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||||||
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# skip these flags when linking the main executable
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if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
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||||||
target_compile_options(lmp PRIVATE ${_FLAG})
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target_compile_options(lmp PRIVATE ${_FLAG})
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||||||
|
endif()
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||||||
endforeach()
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endforeach()
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||||||
########################################################################
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########################################################################
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||||||
# Basic system tests (standard libraries, headers, functions, types) #
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# Basic system tests (standard libraries, headers, functions, types) #
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||||||
@ -838,9 +841,8 @@ if(BUILD_SHARED_LIBS)
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set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
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set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
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||||||
if(Python_EXECUTABLE)
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if(Python_EXECUTABLE)
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||||||
add_custom_target(
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add_custom_target(
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||||||
install-python ${CMAKE_COMMAND} -E remove_directory build
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install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
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||||||
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
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-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} -v ${LAMMPS_SOURCE_DIR}/version.h
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||||||
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
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||||||
COMMENT "Installing LAMMPS Python module")
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COMMENT "Installing LAMMPS Python module")
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||||||
else()
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else()
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||||||
add_custom_target(
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add_custom_target(
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||||||
@ -853,35 +855,6 @@ else()
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|||||||
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
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${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
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||||||
endif()
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endif()
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||||||
|
|
||||||
###############################################################################
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|
||||||
# Add LAMMPS python module to "install" target. This is taylored for building
|
|
||||||
# LAMMPS for package managers and with different prefix settings.
|
|
||||||
# This requires either a shared library or that the PYTHON package is included.
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|
||||||
###############################################################################
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|
||||||
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
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|
||||||
if(CMAKE_VERSION VERSION_LESS 3.12)
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|
||||||
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
|
|
||||||
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
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|
||||||
find_package(PythonInterp) # Deprecated since version 3.12
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|
||||||
if(PYTHONINTERP_FOUND)
|
|
||||||
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
|
|
||||||
endif()
|
|
||||||
else()
|
|
||||||
# backward compatibility
|
|
||||||
if(PYTHON_EXECUTABLE)
|
|
||||||
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
|
|
||||||
endif()
|
|
||||||
find_package(Python COMPONENTS Interpreter)
|
|
||||||
endif()
|
|
||||||
if(Python_EXECUTABLE)
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|
||||||
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
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|
||||||
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
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|
||||||
file(COPY ${LAMMPS_SOURCE_DIR}/version.h DESTINATION ${CMAKE_BINARY_DIR}/python/src)
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|
||||||
file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
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|
||||||
install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
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|
||||||
endif()
|
|
||||||
endif()
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|
||||||
|
|
||||||
include(Testing)
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include(Testing)
|
||||||
include(CodeCoverage)
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include(CodeCoverage)
|
||||||
include(CodingStandard)
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include(CodingStandard)
|
||||||
|
|||||||
@ -60,9 +60,9 @@ if(GPU_API STREQUAL "CUDA")
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|||||||
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
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option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
|
||||||
if(CUDA_MPS_SUPPORT)
|
if(CUDA_MPS_SUPPORT)
|
||||||
if(CUDPP_OPT)
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if(CUDPP_OPT)
|
||||||
message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
|
message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON")
|
||||||
endif()
|
endif()
|
||||||
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
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set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
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set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
|
||||||
@ -98,9 +98,11 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
|
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
|
||||||
if(CUDA_VERSION VERSION_LESS 8.0)
|
if(CUDA_VERSION VERSION_LESS 8.0)
|
||||||
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
|
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
|
||||||
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
|
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
|
||||||
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
|
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
|
||||||
set(GPU_CUDA_GENCODE "-arch=all")
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set(GPU_CUDA_GENCODE "-arch=all")
|
||||||
|
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
|
||||||
|
set(GPU_CUDA_GENCODE "-arch=all")
|
||||||
else()
|
else()
|
||||||
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
|
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
|
||||||
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
|
||||||
@ -175,8 +177,6 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
|
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
target_link_libraries(lammps PRIVATE gpu)
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|
||||||
|
|
||||||
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
||||||
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
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target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
|
||||||
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||||
@ -249,12 +249,12 @@ elseif(GPU_API STREQUAL "OPENCL")
|
|||||||
else()
|
else()
|
||||||
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
|
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
|
||||||
endif()
|
endif()
|
||||||
target_link_libraries(lammps PRIVATE gpu)
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|
||||||
|
|
||||||
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
||||||
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
|
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
|
||||||
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
|
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
|
||||||
add_dependencies(ocl_get_devices OpenCL::OpenCL)
|
add_dependencies(ocl_get_devices OpenCL::OpenCL)
|
||||||
|
|
||||||
elseif(GPU_API STREQUAL "HIP")
|
elseif(GPU_API STREQUAL "HIP")
|
||||||
if(NOT DEFINED HIP_PATH)
|
if(NOT DEFINED HIP_PATH)
|
||||||
if(NOT DEFINED ENV{HIP_PATH})
|
if(NOT DEFINED ENV{HIP_PATH})
|
||||||
@ -285,7 +285,7 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
|
|
||||||
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
|
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
|
||||||
|
|
||||||
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
|
if(HIP_PLATFORM STREQUAL "amd")
|
||||||
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
|
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
|
||||||
elseif(HIP_PLATFORM STREQUAL "spirv")
|
elseif(HIP_PLATFORM STREQUAL "spirv")
|
||||||
set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
|
set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
|
||||||
@ -358,7 +358,7 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
|
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
|
||||||
set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
|
set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
|
||||||
|
|
||||||
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
|
if(HIP_PLATFORM STREQUAL "amd")
|
||||||
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
|
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
|
||||||
|
|
||||||
if(HIP_COMPILER STREQUAL "clang")
|
if(HIP_COMPILER STREQUAL "clang")
|
||||||
@ -412,7 +412,8 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
|
set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
|
||||||
endif()
|
endif()
|
||||||
# add hipCUB
|
# add hipCUB
|
||||||
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
|
find_package(hipcub REQUIRED)
|
||||||
|
target_link_libraries(gpu PRIVATE hip::hipcub)
|
||||||
target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
|
target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
|
||||||
|
|
||||||
if(HIP_PLATFORM STREQUAL "nvcc")
|
if(HIP_PLATFORM STREQUAL "nvcc")
|
||||||
@ -461,34 +462,24 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
|
|
||||||
add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
||||||
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
|
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
|
||||||
target_link_libraries(hip_get_devices hip::host)
|
target_link_libraries(hip_get_devices PRIVATE hip::host)
|
||||||
|
|
||||||
if(HIP_PLATFORM STREQUAL "nvcc")
|
if(HIP_PLATFORM STREQUAL "nvcc")
|
||||||
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
|
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
|
||||||
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
|
|
||||||
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
|
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
|
||||||
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||||
|
|
||||||
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
|
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
|
||||||
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
|
|
||||||
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
|
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
|
||||||
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||||
elseif(HIP_PLATFORM STREQUAL "hcc")
|
endif()
|
||||||
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
|
|
||||||
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
|
|
||||||
|
|
||||||
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
|
|
||||||
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
|
|
||||||
elseif(HIP_PLATFORM STREQUAL "amd")
|
|
||||||
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
|
|
||||||
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
|
|
||||||
|
|
||||||
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
|
|
||||||
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
|
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
|
if(BUILD_OMP)
|
||||||
|
find_package(OpenMP COMPONENTS CXX REQUIRED)
|
||||||
|
target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
|
||||||
|
endif()
|
||||||
target_link_libraries(lammps PRIVATE gpu)
|
target_link_libraries(lammps PRIVATE gpu)
|
||||||
endif()
|
|
||||||
|
|
||||||
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
|
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
|
||||||
# detect styles which have a GPU version
|
# detect styles which have a GPU version
|
||||||
|
|||||||
@ -19,7 +19,7 @@ if(CURL_FOUND)
|
|||||||
target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
|
target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
|
option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
|
||||||
mark_as_advanced(KIM_EXTRA_UNITTESTS)
|
mark_as_advanced(KIM_EXTRA_UNITTESTS)
|
||||||
find_package(PkgConfig QUIET)
|
find_package(PkgConfig QUIET)
|
||||||
set(DOWNLOAD_KIM_DEFAULT ON)
|
set(DOWNLOAD_KIM_DEFAULT ON)
|
||||||
|
|||||||
@ -72,13 +72,11 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
|
set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
|
||||||
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
|
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
|
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
|
||||||
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
|
|
||||||
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
|
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
|
||||||
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
|
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
|
||||||
elseif(EXTERNAL_KOKKOS)
|
elseif(EXTERNAL_KOKKOS)
|
||||||
find_package(Kokkos 3.7.01 REQUIRED CONFIG)
|
find_package(Kokkos 3.7.01 REQUIRED CONFIG)
|
||||||
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
||||||
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
|
|
||||||
else()
|
else()
|
||||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||||
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
|
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
|
||||||
@ -98,7 +96,6 @@ else()
|
|||||||
${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||||
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
|
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
|
||||||
target_link_libraries(lammps PRIVATE kokkos)
|
target_link_libraries(lammps PRIVATE kokkos)
|
||||||
target_link_libraries(lmp PRIVATE kokkos)
|
|
||||||
if(BUILD_SHARED_LIBS_WAS_ON)
|
if(BUILD_SHARED_LIBS_WAS_ON)
|
||||||
set(BUILD_SHARED_LIBS ON)
|
set(BUILD_SHARED_LIBS ON)
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
|
|||||||
|
|
||||||
if(DOWNLOAD_MDI)
|
if(DOWNLOAD_MDI)
|
||||||
message(STATUS "MDI download requested - we will build our own")
|
message(STATUS "MDI download requested - we will build our own")
|
||||||
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
|
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
|
||||||
set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
|
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
|
||||||
mark_as_advanced(MDI_URL)
|
mark_as_advanced(MDI_URL)
|
||||||
mark_as_advanced(MDI_MD5)
|
mark_as_advanced(MDI_MD5)
|
||||||
GetFallbackURL(MDI_URL MDI_FALLBACK)
|
GetFallbackURL(MDI_URL MDI_FALLBACK)
|
||||||
|
|||||||
@ -7,8 +7,8 @@ else()
|
|||||||
endif()
|
endif()
|
||||||
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
|
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
|
||||||
if(DOWNLOAD_MSCG)
|
if(DOWNLOAD_MSCG)
|
||||||
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
|
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
|
||||||
set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
|
set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
|
||||||
mark_as_advanced(MSCG_URL)
|
mark_as_advanced(MSCG_URL)
|
||||||
mark_as_advanced(MSCG_MD5)
|
mark_as_advanced(MSCG_MD5)
|
||||||
|
|
||||||
|
|||||||
@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
|
|||||||
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
|
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
|
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz" CACHE STRING "URL for PLUMED tarball")
|
||||||
set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
|
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
|
||||||
|
|
||||||
mark_as_advanced(PLUMED_URL)
|
mark_as_advanced(PLUMED_URL)
|
||||||
mark_as_advanced(PLUMED_MD5)
|
mark_as_advanced(PLUMED_MD5)
|
||||||
|
|||||||
@ -104,6 +104,7 @@ function(RegisterStyles search_path)
|
|||||||
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
|
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
|
||||||
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
|
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
|
||||||
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
|
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
|
||||||
|
FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
|
||||||
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
|
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
|
||||||
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
|
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
|
||||||
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
|
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
|
||||||
@ -127,6 +128,7 @@ function(RegisterStylesExt search_path extension sources)
|
|||||||
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
|
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
|
||||||
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
|
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
|
||||||
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
|
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
|
||||||
|
FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension} GRAN_SUB_MOD ${sources})
|
||||||
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
|
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
|
||||||
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
|
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
|
||||||
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
|
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
|
||||||
@ -151,6 +153,7 @@ function(GenerateStyleHeaders output_path)
|
|||||||
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
|
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
|
||||||
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
|
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
|
||||||
GenerateStyleHeader(${output_path} FIX fix ) # modify
|
GenerateStyleHeader(${output_path} FIX fix ) # modify
|
||||||
|
GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
|
||||||
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
|
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
|
||||||
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
|
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
|
||||||
GenerateStyleHeader(${output_path} KSPACE kspace ) # force
|
GenerateStyleHeader(${output_path} KSPACE kspace ) # force
|
||||||
|
|||||||
17
doc/Makefile
17
doc/Makefile
@ -94,10 +94,11 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
|||||||
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
||||||
rst_anchor_check src/*.rst ;\
|
rst_anchor_check src/*.rst ;\
|
||||||
python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
|
$(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
|
||||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||||
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
|
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
|
||||||
python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
|
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
|
||||||
|
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
|
||||||
echo "############################################" ;\
|
echo "############################################" ;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
@ -174,10 +175,11 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
|
|||||||
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
||||||
rst_anchor_check src/*.rst ;\
|
rst_anchor_check src/*.rst ;\
|
||||||
python utils/check-packages.py -s ../src -d src ;\
|
$(PYTHON) utils/check-packages.py -s ../src -d src ;\
|
||||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||||
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
|
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
|
||||||
python utils/check-styles.py -s ../src -d src ;\
|
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
|
||||||
|
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
|
||||||
echo "############################################" ;\
|
echo "############################################" ;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
@ -208,14 +210,14 @@ anchor_check : $(ANCHORCHECK)
|
|||||||
style_check : $(VENV)
|
style_check : $(VENV)
|
||||||
@(\
|
@(\
|
||||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
||||||
python utils/check-styles.py -s ../src -d src ;\
|
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
|
|
||||||
package_check : $(VENV)
|
package_check : $(VENV)
|
||||||
@(\
|
@(\
|
||||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \\
|
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
|
||||||
python utils/check-packages.py -s ../src -d src ;\
|
$(PYTHON) utils/check-packages.py -s ../src -d src ;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
|
|
||||||
@ -224,6 +226,7 @@ char_check :
|
|||||||
|
|
||||||
role_check :
|
role_check :
|
||||||
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
|
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
|
||||||
|
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
|
||||||
|
|
||||||
link_check : $(VENV) html
|
link_check : $(VENV) html
|
||||||
@(\
|
@(\
|
||||||
|
|||||||
@ -123,7 +123,7 @@ request is merged. The template for pull requests includes a header
|
|||||||
where connections between pull requests and issues can be listed, and
|
where connections between pull requests and issues can be listed, and
|
||||||
thus where this comment should be placed.
|
thus where this comment should be placed.
|
||||||
|
|
||||||
## Milestones and Release Planning
|
## Release Planning
|
||||||
|
|
||||||
LAMMPS uses a continuous release development model with incremental
|
LAMMPS uses a continuous release development model with incremental
|
||||||
changes, i.e. significant effort is made -- including automated pre-merge
|
changes, i.e. significant effort is made -- including automated pre-merge
|
||||||
@ -132,24 +132,28 @@ broken. These tests are run after every update to a pull request. More
|
|||||||
extensive and time-consuming tests (including regression testing) are
|
extensive and time-consuming tests (including regression testing) are
|
||||||
performed after code is merged to the "develop" branch. There are feature
|
performed after code is merged to the "develop" branch. There are feature
|
||||||
releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
|
releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
|
||||||
developers feel, that a sufficient number of changes has been included
|
developers feel, that a sufficient number of changes have been included
|
||||||
and all post-merge testing has been successful. These feature releases are
|
and all post-merge testing has been successful. These feature releases are
|
||||||
marked with a `patch_<version date>` tag and the "release" branch
|
marked with a `patch_<version date>` tag and the "release" branch
|
||||||
follows only these versions with fast-forward merges. While "develop" may
|
follows only these versions with fast-forward merges. While "develop" may
|
||||||
be temporarily broken through issues only detected by the post-merge tests,
|
be temporarily broken through issues only detected by the post-merge tests,
|
||||||
The "release" branch is always supposed to be of production quality.
|
The "release" branch is always supposed to be of production quality.
|
||||||
|
|
||||||
About once each year, there is a "stable" release of LAMMPS.
|
About once each year, there is a "stable" release of LAMMPS. These have
|
||||||
These have seen additional, manual testing and review of
|
seen additional, manual testing and review of results from testing with
|
||||||
results from testing with instrumented code and static code analysis.
|
instrumented code and static code analysis. Also, the last few feature
|
||||||
Also, the last few feature releases before a stable release are "release
|
releases before a stable release are "release candidate" versions which
|
||||||
candidate" versions which only contain bug fixes, feature additions to
|
only contain bug fixes, feature additions to peripheral functionality,
|
||||||
peripheral functionality, and documentation updates. In between stable
|
and documentation updates. In between stable releases, bug fixes and
|
||||||
releases, bug fixes and infrastructure updates are back-ported from the
|
infrastructure updates are back-ported from the "develop" branch to the
|
||||||
"develop" branch to the "maintenance" branch and occasionally merged
|
"maintenance" branch and occasionally merged into "stable" and published
|
||||||
into "stable" and published as update releases.
|
as update releases.
|
||||||
|
|
||||||
|
## Project Management
|
||||||
|
|
||||||
For release planning and the information of code contributors, issues
|
For release planning and the information of code contributors, issues
|
||||||
and pull requests being actively worked on are assigned a "milestone",
|
and pull requests are being managed with GitHub Project Boards. There
|
||||||
which corresponds to the next stable release or the stable release after
|
are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
|
||||||
that, with a tentative release date.
|
and LAMMPS Pull Requests. Each board is organized in columns where
|
||||||
|
submissions are categorized. Within each column the entries are
|
||||||
|
(manually) sorted according their priority.
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.TH LAMMPS "1" "8 February 2023" "2023-02-08"
|
.TH LAMMPS "1" "28 March 2023" "2023-03-28"
|
||||||
.SH NAME
|
.SH NAME
|
||||||
.B LAMMPS
|
.B LAMMPS
|
||||||
\- Molecular Dynamics Simulator. Version 8 February 2023
|
\- Molecular Dynamics Simulator. Version 28 March 2023
|
||||||
|
|
||||||
.SH SYNOPSIS
|
.SH SYNOPSIS
|
||||||
.B lmp
|
.B lmp
|
||||||
|
|||||||
@ -1,11 +1,11 @@
|
|||||||
.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
|
.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
|
||||||
.SH NAME
|
.SH NAME
|
||||||
.B MSI2LMP
|
.B MSI2LMP
|
||||||
\- Converter for Materials Studio files to LAMMPS
|
\- Converter for Materials Studio files to LAMMPS
|
||||||
|
|
||||||
.SH SYNOPSIS
|
.SH SYNOPSIS
|
||||||
.B msi2lmp
|
.B msi2lmp
|
||||||
<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
|
[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
|
||||||
|
|
||||||
.SH DESCRIPTION
|
.SH DESCRIPTION
|
||||||
.PP
|
.PP
|
||||||
@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
|
|||||||
|
|
||||||
.SH OPTIONS
|
.SH OPTIONS
|
||||||
.TP
|
.TP
|
||||||
|
\fB\-h\fR, \fB\-help\fR,
|
||||||
|
Print detailed help message to the screen and stop.
|
||||||
|
.TP
|
||||||
\fB\<ROOTNAME>\fR
|
\fB\<ROOTNAME>\fR
|
||||||
This has to be the first argument and is a
|
This has to be the first argument and is a
|
||||||
.B mandatory
|
.B mandatory
|
||||||
|
|||||||
@ -523,6 +523,8 @@ The following options are available.
|
|||||||
These should help to make source and documentation files conforming
|
These should help to make source and documentation files conforming
|
||||||
to some the coding style preferences of the LAMMPS developers.
|
to some the coding style preferences of the LAMMPS developers.
|
||||||
|
|
||||||
|
.. _clang-format:
|
||||||
|
|
||||||
Clang-format support
|
Clang-format support
|
||||||
--------------------
|
--------------------
|
||||||
|
|
||||||
|
|||||||
@ -180,6 +180,9 @@ way no local OpenCL development headers or library needs to be present and only
|
|||||||
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
|
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
|
||||||
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
|
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
|
||||||
|
|
||||||
|
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
|
||||||
|
with ``-D BUILD_OMP=on`` this will also be enabled.
|
||||||
|
|
||||||
If you are compiling with HIP, note that before running CMake you will have to
|
If you are compiling with HIP, note that before running CMake you will have to
|
||||||
set appropriate environment variables. Some variables such as
|
set appropriate environment variables. Some variables such as
|
||||||
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
|
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
|
||||||
@ -273,10 +276,13 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable
|
|||||||
most modern GPUs.
|
most modern GPUs.
|
||||||
|
|
||||||
To support the CUDA multiprocessor server you can set the define
|
To support the CUDA multiprocessor server you can set the define
|
||||||
``-DCUDA_PROXY``. Please note that in this case you must **not** use
|
``-DCUDA_MPS_SUPPORT``. Please note that in this case you must **not** use
|
||||||
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
|
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
|
||||||
to empty.
|
to empty.
|
||||||
|
|
||||||
|
The GPU library has some multi-thread support using OpenMP. You need to add
|
||||||
|
the compiler flag that enables OpenMP to the ``CUDR_OPTS`` Makefile variable.
|
||||||
|
|
||||||
If the library build is successful, 3 files should be created:
|
If the library build is successful, 3 files should be created:
|
||||||
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
|
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
|
||||||
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS
|
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS
|
||||||
@ -1906,10 +1912,10 @@ OPENMP package
|
|||||||
Apple offers the `Xcode package and IDE
|
Apple offers the `Xcode package and IDE
|
||||||
<https://developer.apple.com/xcode/>`_ for compiling software on
|
<https://developer.apple.com/xcode/>`_ for compiling software on
|
||||||
macOS, so you have likely installed it to compile LAMMPS. Their
|
macOS, so you have likely installed it to compile LAMMPS. Their
|
||||||
compiler is based on `Clang <https://clang.llvm.org/>`, but while it
|
compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
|
||||||
is capable of processing OpenMP directives, the necessary header
|
is capable of processing OpenMP directives, the necessary header
|
||||||
files and OpenMP runtime library are missing. The `R developers
|
files and OpenMP runtime library are missing. The `R developers
|
||||||
<https://www.r-project.org/>` have figured out a way to build those
|
<https://www.r-project.org/>`_ have figured out a way to build those
|
||||||
in a compatible fashion. One can download them from
|
in a compatible fashion. One can download them from
|
||||||
`https://mac.r-project.org/openmp/
|
`https://mac.r-project.org/openmp/
|
||||||
<https://mac.r-project.org/openmp/>`_. Simply adding those files as
|
<https://mac.r-project.org/openmp/>`_. Simply adding those files as
|
||||||
|
|||||||
@ -42,6 +42,7 @@ OPT.
|
|||||||
* :doc:`gaussian <bond_gaussian>`
|
* :doc:`gaussian <bond_gaussian>`
|
||||||
* :doc:`gromos (o) <bond_gromos>`
|
* :doc:`gromos (o) <bond_gromos>`
|
||||||
* :doc:`harmonic (iko) <bond_harmonic>`
|
* :doc:`harmonic (iko) <bond_harmonic>`
|
||||||
|
* :doc:`harmonic/restrain <bond_harmonic_restrain>`
|
||||||
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
|
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
|
||||||
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
|
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
|
||||||
* :doc:`lepton (o) <bond_lepton>`
|
* :doc:`lepton (o) <bond_lepton>`
|
||||||
|
|||||||
@ -52,6 +52,8 @@ KOKKOS, o = OPENMP, t = OPT.
|
|||||||
* :doc:`dilatation/atom <compute_dilatation_atom>`
|
* :doc:`dilatation/atom <compute_dilatation_atom>`
|
||||||
* :doc:`dipole <compute_dipole>`
|
* :doc:`dipole <compute_dipole>`
|
||||||
* :doc:`dipole/chunk <compute_dipole_chunk>`
|
* :doc:`dipole/chunk <compute_dipole_chunk>`
|
||||||
|
* :doc:`dipole/tip4p <compute_dipole>`
|
||||||
|
* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
|
||||||
* :doc:`displace/atom <compute_displace_atom>`
|
* :doc:`displace/atom <compute_displace_atom>`
|
||||||
* :doc:`dpd <compute_dpd>`
|
* :doc:`dpd <compute_dpd>`
|
||||||
* :doc:`dpd/atom <compute_dpd_atom>`
|
* :doc:`dpd/atom <compute_dpd_atom>`
|
||||||
@ -104,6 +106,7 @@ KOKKOS, o = OPENMP, t = OPT.
|
|||||||
* :doc:`pe/tally <compute_tally>`
|
* :doc:`pe/tally <compute_tally>`
|
||||||
* :doc:`plasticity/atom <compute_plasticity_atom>`
|
* :doc:`plasticity/atom <compute_plasticity_atom>`
|
||||||
* :doc:`pressure <compute_pressure>`
|
* :doc:`pressure <compute_pressure>`
|
||||||
|
* :doc:`pressure/alchemy <compute_pressure_alchemy>`
|
||||||
* :doc:`pressure/uef <compute_pressure_uef>`
|
* :doc:`pressure/uef <compute_pressure_uef>`
|
||||||
* :doc:`property/atom <compute_property_atom>`
|
* :doc:`property/atom <compute_property_atom>`
|
||||||
* :doc:`property/chunk <compute_property_chunk>`
|
* :doc:`property/chunk <compute_property_chunk>`
|
||||||
|
|||||||
@ -29,6 +29,7 @@ OPT.
|
|||||||
* :doc:`adapt/fep <fix_adapt_fep>`
|
* :doc:`adapt/fep <fix_adapt_fep>`
|
||||||
* :doc:`addforce <fix_addforce>`
|
* :doc:`addforce <fix_addforce>`
|
||||||
* :doc:`addtorque <fix_addtorque>`
|
* :doc:`addtorque <fix_addtorque>`
|
||||||
|
* :doc:`alchemy <fix_alchemy>`
|
||||||
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
|
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
|
||||||
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
|
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
|
||||||
* :doc:`append/atoms <fix_append_atoms>`
|
* :doc:`append/atoms <fix_append_atoms>`
|
||||||
@ -69,6 +70,7 @@ OPT.
|
|||||||
* :doc:`dt/reset (k) <fix_dt_reset>`
|
* :doc:`dt/reset (k) <fix_dt_reset>`
|
||||||
* :doc:`edpd/source <fix_dpd_source>`
|
* :doc:`edpd/source <fix_dpd_source>`
|
||||||
* :doc:`efield <fix_efield>`
|
* :doc:`efield <fix_efield>`
|
||||||
|
* :doc:`efield/tip4p <fix_efield>`
|
||||||
* :doc:`ehex <fix_ehex>`
|
* :doc:`ehex <fix_ehex>`
|
||||||
* :doc:`electrode/conp (i) <fix_electrode>`
|
* :doc:`electrode/conp (i) <fix_electrode>`
|
||||||
* :doc:`electrode/conq (i) <fix_electrode>`
|
* :doc:`electrode/conq (i) <fix_electrode>`
|
||||||
@ -92,6 +94,7 @@ OPT.
|
|||||||
* :doc:`grem <fix_grem>`
|
* :doc:`grem <fix_grem>`
|
||||||
* :doc:`halt <fix_halt>`
|
* :doc:`halt <fix_halt>`
|
||||||
* :doc:`heat <fix_heat>`
|
* :doc:`heat <fix_heat>`
|
||||||
|
* :doc:`heat/flow <fix_heat_flow>`
|
||||||
* :doc:`hyper/global <fix_hyper_global>`
|
* :doc:`hyper/global <fix_hyper_global>`
|
||||||
* :doc:`hyper/local <fix_hyper_local>`
|
* :doc:`hyper/local <fix_hyper_local>`
|
||||||
* :doc:`imd <fix_imd>`
|
* :doc:`imd <fix_imd>`
|
||||||
@ -107,6 +110,7 @@ OPT.
|
|||||||
* :doc:`lineforce <fix_lineforce>`
|
* :doc:`lineforce <fix_lineforce>`
|
||||||
* :doc:`manifoldforce <fix_manifoldforce>`
|
* :doc:`manifoldforce <fix_manifoldforce>`
|
||||||
* :doc:`mdi/qm <fix_mdi_qm>`
|
* :doc:`mdi/qm <fix_mdi_qm>`
|
||||||
|
* :doc:`mdi/qmmm <fix_mdi_qmmm>`
|
||||||
* :doc:`meso/move <fix_meso_move>`
|
* :doc:`meso/move <fix_meso_move>`
|
||||||
* :doc:`mol/swap <fix_mol_swap>`
|
* :doc:`mol/swap <fix_mol_swap>`
|
||||||
* :doc:`momentum (k) <fix_momentum>`
|
* :doc:`momentum (k) <fix_momentum>`
|
||||||
@ -262,6 +266,7 @@ OPT.
|
|||||||
* :doc:`wall/lj1043 <fix_wall>`
|
* :doc:`wall/lj1043 <fix_wall>`
|
||||||
* :doc:`wall/lj126 <fix_wall>`
|
* :doc:`wall/lj126 <fix_wall>`
|
||||||
* :doc:`wall/lj93 (k) <fix_wall>`
|
* :doc:`wall/lj93 (k) <fix_wall>`
|
||||||
|
* :doc:`wall/lepton <fix_wall>`
|
||||||
* :doc:`wall/morse <fix_wall>`
|
* :doc:`wall/morse <fix_wall>`
|
||||||
* :doc:`wall/piston <fix_wall_piston>`
|
* :doc:`wall/piston <fix_wall_piston>`
|
||||||
* :doc:`wall/reflect (k) <fix_wall_reflect>`
|
* :doc:`wall/reflect (k) <fix_wall_reflect>`
|
||||||
@ -269,4 +274,5 @@ OPT.
|
|||||||
* :doc:`wall/region <fix_wall_region>`
|
* :doc:`wall/region <fix_wall_region>`
|
||||||
* :doc:`wall/region/ees <fix_wall_ees>`
|
* :doc:`wall/region/ees <fix_wall_ees>`
|
||||||
* :doc:`wall/srd <fix_wall_srd>`
|
* :doc:`wall/srd <fix_wall_srd>`
|
||||||
|
* :doc:`wall/table <fix_wall>`
|
||||||
* :doc:`widom <fix_widom>`
|
* :doc:`widom <fix_widom>`
|
||||||
|
|||||||
@ -55,6 +55,7 @@ OPT.
|
|||||||
* :doc:`born/coul/msm (o) <pair_born>`
|
* :doc:`born/coul/msm (o) <pair_born>`
|
||||||
* :doc:`born/coul/wolf (go) <pair_born>`
|
* :doc:`born/coul/wolf (go) <pair_born>`
|
||||||
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
|
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
|
||||||
|
* :doc:`born/gauss <pair_born_gauss>`
|
||||||
* :doc:`bpm/spring <pair_bpm_spring>`
|
* :doc:`bpm/spring <pair_bpm_spring>`
|
||||||
* :doc:`brownian (o) <pair_brownian>`
|
* :doc:`brownian (o) <pair_brownian>`
|
||||||
* :doc:`brownian/poly (o) <pair_brownian>`
|
* :doc:`brownian/poly (o) <pair_brownian>`
|
||||||
|
|||||||
@ -11,6 +11,7 @@ Available topics are:
|
|||||||
|
|
||||||
- `Reading and parsing of text and text files`_
|
- `Reading and parsing of text and text files`_
|
||||||
- `Requesting and accessing neighbor lists`_
|
- `Requesting and accessing neighbor lists`_
|
||||||
|
- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
|
||||||
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
|
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
|
||||||
- `KSpace PPPM FFT grids`_
|
- `KSpace PPPM FFT grids`_
|
||||||
|
|
||||||
@ -73,6 +74,8 @@ when converting "12.5", while the ValueTokenizer class will throw an
|
|||||||
:cpp:func:`ValueTokenizer::next_int()
|
:cpp:func:`ValueTokenizer::next_int()
|
||||||
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
|
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
|
||||||
|
|
||||||
|
.. _request-neighbor-list:
|
||||||
|
|
||||||
Requesting and accessing neighbor lists
|
Requesting and accessing neighbor lists
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
@ -216,6 +219,30 @@ command:
|
|||||||
|
|
||||||
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
|
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
|
||||||
|
|
||||||
|
Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
There are multiple ways to manage per-atom data within LAMMPS. Often
|
||||||
|
the per-atom storage is only used locally and managed by the class that
|
||||||
|
uses it. If the data has to persist between multiple time steps and
|
||||||
|
migrate with atoms when they move from sub-domain to sub-domain or
|
||||||
|
across periodic boundaries, then using a custom atom style, or :doc:`fix
|
||||||
|
property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
|
||||||
|
possible options.
|
||||||
|
|
||||||
|
- Using the atom style is usually the most programming effort and mostly
|
||||||
|
needed when the per-atom data is an integral part of the model like a
|
||||||
|
per-atom charge or diameter and thus should be part of the Atoms
|
||||||
|
section of a :doc:`data file <read_data>`.
|
||||||
|
|
||||||
|
- Fix property/atom is useful if the data is optional or should be
|
||||||
|
entered by the user, or accessed as a (named) custom property. In this
|
||||||
|
case the fix should be entered as part of the input (and not
|
||||||
|
internally) which allows to enter and store its content with data files.
|
||||||
|
|
||||||
|
- Fix STORE/ATOM should be used when the data should be accessed internally
|
||||||
|
only and thus the fix can be created internally.
|
||||||
|
|
||||||
Fix contributions to instantaneous energy, virial, and cumulative energy
|
Fix contributions to instantaneous energy, virial, and cumulative energy
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
|||||||
@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
|
|||||||
- `Use of "override" instead of "virtual"`_
|
- `Use of "override" instead of "virtual"`_
|
||||||
- `Simplified and more compact neighbor list requests`_
|
- `Simplified and more compact neighbor list requests`_
|
||||||
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
|
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
|
||||||
|
- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
|
||||||
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
|
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
|
||||||
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
|
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
|
||||||
|
|
||||||
@ -385,6 +386,34 @@ New:
|
|||||||
|
|
||||||
This change is **required** or else the code will not compile.
|
This change is **required** or else the code will not compile.
|
||||||
|
|
||||||
|
Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
.. versionchanged:: 28Mar2023
|
||||||
|
|
||||||
|
The available functionality of the internal fix to store per-atom
|
||||||
|
properties was expanded to enable storing data with ghost atoms and to
|
||||||
|
support binary restart files. With those changes, the fix was renamed
|
||||||
|
to fix STORE/ATOM and the number and order of (required) arguments has
|
||||||
|
changed.
|
||||||
|
|
||||||
|
Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
|
||||||
|
|
||||||
|
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
|
||||||
|
- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
|
||||||
|
- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
|
||||||
|
- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
|
||||||
|
|
||||||
|
New syntax: ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
|
||||||
|
|
||||||
|
- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
|
||||||
|
- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
|
||||||
|
- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
|
||||||
|
- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
|
||||||
|
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
|
||||||
|
|
||||||
|
Since this is an internal fix, there is no user visible change.
|
||||||
|
|
||||||
Use Output::get_dump_by_id() instead of Output::find_dump()
|
Use Output::get_dump_by_id() instead of Output::find_dump()
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
|||||||
@ -6,250 +6,8 @@ be extended by writing new classes that derive from existing
|
|||||||
parent classes in LAMMPS. Here, some specific coding
|
parent classes in LAMMPS. Here, some specific coding
|
||||||
details are provided for writing code for LAMMPS.
|
details are provided for writing code for LAMMPS.
|
||||||
|
|
||||||
Writing a new fix style
|
.. toctree::
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^
|
:maxdepth: 1
|
||||||
|
|
||||||
Writing fixes is a flexible way of extending LAMMPS. Users can
|
|
||||||
implement many things using fixes:
|
|
||||||
|
|
||||||
- changing particles attributes (positions, velocities, forces, etc.). Examples: FixNVE, FixFreeze.
|
|
||||||
- reading/writing data. Example: FixRestart.
|
|
||||||
- adding or modifying properties due to geometry. Example: FixWall.
|
|
||||||
- interacting with other subsystems or external code: Examples: FixTTM, FixExternal
|
|
||||||
- saving information for analysis or future use (previous positions,
|
|
||||||
for instance). Examples: Fix AveTime, FixStoreState.
|
|
||||||
|
|
||||||
|
|
||||||
All fixes are derived from the Fix base class and must have a
|
|
||||||
constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
|
|
||||||
|
|
||||||
Every fix must be registered in LAMMPS by writing the following lines
|
|
||||||
of code in the header before include guards:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
#ifdef FIX_CLASS
|
|
||||||
// clang-format off
|
|
||||||
FixStyle(print/vel,FixPrintVel);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
/* the definition of the FixPrintVel class comes here */
|
|
||||||
...
|
|
||||||
#endif
|
|
||||||
|
|
||||||
Where ``print/vel`` is the style name of your fix in the input script and
|
|
||||||
``FixPrintVel`` is the name of the class. The header file would be called
|
|
||||||
``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
|
|
||||||
These conventions allow LAMMPS to automatically integrate it into the
|
|
||||||
executable when compiling and associate your new fix class with the designated
|
|
||||||
keyword when it parses the input script.
|
|
||||||
|
|
||||||
Let's write a simple fix which will print the average velocity at the end
|
|
||||||
of each timestep. First of all, implement a constructor:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
|
|
||||||
: Fix(lmp, narg, arg)
|
|
||||||
{
|
|
||||||
if (narg < 4)
|
|
||||||
error->all(FLERR,"Illegal fix print/vel command");
|
|
||||||
|
|
||||||
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
|
|
||||||
if (nevery <= 0)
|
|
||||||
error->all(FLERR,"Illegal fix print/vel command");
|
|
||||||
}
|
|
||||||
|
|
||||||
In the constructor you should parse your fix arguments which are
|
|
||||||
specified in the script. All fixes have pretty much the same syntax:
|
|
||||||
``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The
|
|
||||||
first 3 parameters are parsed by Fix base class constructor, while
|
|
||||||
``<fix arguments>`` should be parsed by you. In our case, we need to
|
|
||||||
specify how often we want to print an average velocity. For instance,
|
|
||||||
once in 50 timesteps: ``fix 1 print/vel 50``. There is a special variable
|
|
||||||
in the Fix class called ``nevery`` which specifies how often the method
|
|
||||||
``end_of_step()`` is called. Thus all we need to do is just set it up.
|
|
||||||
|
|
||||||
The next method we need to implement is ``setmask()``:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
int FixPrintVel::setmask()
|
|
||||||
{
|
|
||||||
int mask = 0;
|
|
||||||
mask |= FixConst::END_OF_STEP;
|
|
||||||
return mask;
|
|
||||||
}
|
|
||||||
|
|
||||||
Here the user specifies which methods of your fix should be called
|
|
||||||
during execution. The constant ``END_OF_STEP`` corresponds to the
|
|
||||||
``end_of_step()`` method. The most important available methods that
|
|
||||||
are called during a timestep and the order in which they are called
|
|
||||||
are shown in the previous section.
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
void FixPrintVel::end_of_step()
|
|
||||||
{
|
|
||||||
// for add3, scale3
|
|
||||||
using namespace MathExtra;
|
|
||||||
|
|
||||||
double** v = atom->v;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
double localAvgVel[4]; // 4th element for particles count
|
|
||||||
memset(localAvgVel, 0, 4 * sizeof(double));
|
|
||||||
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
|
||||||
add3(localAvgVel, v[particleInd], localAvgVel);
|
|
||||||
}
|
|
||||||
localAvgVel[3] = nlocal;
|
|
||||||
double globalAvgVel[4];
|
|
||||||
memset(globalAvgVel, 0, 4 * sizeof(double));
|
|
||||||
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
scale3(1.0 / globalAvgVel[3], globalAvgVel);
|
|
||||||
if ((comm->me == 0) && screen) {
|
|
||||||
fmt::print(screen,"{}, {}, {}\n",
|
|
||||||
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
In the code above, we use MathExtra routines defined in
|
|
||||||
``math_extra.h``. There are bunch of math functions to work with
|
|
||||||
arrays of doubles as with math vectors. It is also important to note
|
|
||||||
that LAMMPS code should always assume to be run in parallel and that
|
|
||||||
atom data is thus distributed across the MPI ranks. Thus you can
|
|
||||||
only process data from local atoms directly and need to use MPI library
|
|
||||||
calls to combine or exchange data. For serial execution, LAMMPS
|
|
||||||
comes bundled with the MPI STUBS library that contains the MPI library
|
|
||||||
function calls in dummy versions that only work for a single MPI rank.
|
|
||||||
|
|
||||||
In this code we use an instance of Atom class. This object is stored
|
|
||||||
in the Pointers class (see ``pointers.h``) which is the base class of
|
|
||||||
the Fix base class. This object contains references to various class
|
|
||||||
instances (the original instances are created and held by the LAMMPS
|
|
||||||
class) with all global information about the simulation system.
|
|
||||||
Data from the Pointers class is available to all classes inherited from
|
|
||||||
it using protected inheritance. Hence when you write you own class,
|
|
||||||
which is going to use LAMMPS data, don't forget to inherit from Pointers
|
|
||||||
or pass an Pointer to it to all functions that need access. When writing
|
|
||||||
fixes we inherit from class Fix which is inherited from Pointers so
|
|
||||||
there is no need to inherit from it directly.
|
|
||||||
|
|
||||||
The code above computes average velocity for all particles in the
|
|
||||||
simulation. Yet you have one unused parameter in fix call from the
|
|
||||||
script: ``group_name``. This parameter specifies the group of atoms
|
|
||||||
used in the fix. So we should compute average for all particles in the
|
|
||||||
simulation only if ``group_name == "all"``, but it can be any group.
|
|
||||||
The group membership information of an atom is contained in the *mask*
|
|
||||||
property of and atom and the bit corresponding to a given group is
|
|
||||||
stored in the groupbit variable which is defined in Fix base class:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; ++i) {
|
|
||||||
if (atom->mask[i] & groupbit) {
|
|
||||||
// Do all job here
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
Class Atom encapsulates atoms positions, velocities, forces, etc. User
|
|
||||||
can access them using particle index. Note, that particle indexes are
|
|
||||||
usually changed every few timesteps because of neighbor list rebuilds
|
|
||||||
and spatial sorting (to improve cache efficiency).
|
|
||||||
|
|
||||||
Let us consider another Fix example: We want to have a fix which stores
|
|
||||||
atoms position from previous time step in your fix. The local atoms
|
|
||||||
indexes may not be valid on the next iteration. In order to handle
|
|
||||||
this situation there are several methods which should be implemented:
|
|
||||||
|
|
||||||
- ``double memory_usage()``: return how much memory the fix uses (optional)
|
|
||||||
- ``void grow_arrays(int)``: do reallocation of the per particle arrays in your fix
|
|
||||||
- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
|
|
||||||
information to j-th. Used when atom sorting is performed. if delflag is set
|
|
||||||
and atom j owns a body, move the body information to atom i.
|
|
||||||
- ``void set_arrays(int i)``: sets i-th particle related information to zero
|
|
||||||
|
|
||||||
Note, that if your class implements these methods, it must call add calls of
|
|
||||||
add_callback and delete_callback to constructor and destructor. Since we want
|
|
||||||
to store positions of atoms from previous timestep, we need to add
|
|
||||||
``double** xold`` to the header file. Than add allocation code
|
|
||||||
to the constructor:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
|
|
||||||
{
|
|
||||||
//...
|
|
||||||
memory->create(xold, atom->nmax, 3, "FixSavePos:x");
|
|
||||||
atom->add_callback(0);
|
|
||||||
}
|
|
||||||
|
|
||||||
FixSavePos::~FixSavePos() {
|
|
||||||
atom->delete_callback(id, 0);
|
|
||||||
memory->destroy(xold);
|
|
||||||
}
|
|
||||||
|
|
||||||
Implement the aforementioned methods:
|
|
||||||
|
|
||||||
.. code-block:: c++
|
|
||||||
|
|
||||||
double FixSavePos::memory_usage()
|
|
||||||
{
|
|
||||||
int nmax = atom->nmax;
|
|
||||||
double bytes = 0.0;
|
|
||||||
bytes += nmax * 3 * sizeof(double);
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::grow_arrays(int nmax)
|
|
||||||
{
|
|
||||||
memory->grow(xold, nmax, 3, "FixSavePos:xold");
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::copy_arrays(int i, int j, int delflag)
|
|
||||||
{
|
|
||||||
memcpy(xold[j], xold[i], sizeof(double) * 3);
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::set_arrays(int i)
|
|
||||||
{
|
|
||||||
memset(xold[i], 0, sizeof(double) * 3);
|
|
||||||
}
|
|
||||||
|
|
||||||
int FixSavePos::pack_exchange(int i, double *buf)
|
|
||||||
{
|
|
||||||
int m = 0;
|
|
||||||
buf[m++] = xold[i][0];
|
|
||||||
buf[m++] = xold[i][1];
|
|
||||||
buf[m++] = xold[i][2];
|
|
||||||
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
|
|
||||||
int FixSavePos::unpack_exchange(int nlocal, double *buf)
|
|
||||||
{
|
|
||||||
int m = 0;
|
|
||||||
xold[nlocal][0] = buf[m++];
|
|
||||||
xold[nlocal][1] = buf[m++];
|
|
||||||
xold[nlocal][2] = buf[m++];
|
|
||||||
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
|
|
||||||
Now, a little bit about memory allocation. We use the Memory class which
|
|
||||||
is just a bunch of template functions for allocating 1D and 2D
|
|
||||||
arrays. So you need to add include ``memory.h`` to have access to them.
|
|
||||||
|
|
||||||
Finally, if you need to write/read some global information used in
|
|
||||||
your fix to the restart file, you might do it by setting flag
|
|
||||||
``restart_global = 1`` in the constructor and implementing methods void
|
|
||||||
``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
|
|
||||||
If, in addition, you want to write the per-atom property to restart
|
|
||||||
files additional settings and functions are needed:
|
|
||||||
|
|
||||||
- a fix flag indicating this needs to be set ``restart_peratom = 1;``
|
|
||||||
- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
|
|
||||||
a second time with the final argument set to 1 instead of 0 (indicating
|
|
||||||
restart processing instead of per-atom data memory management).
|
|
||||||
- the functions ``void pack_restart(int i, double *buf)`` and
|
|
||||||
``void unpack_restart(int nlocal, int nth)`` need to be implemented
|
|
||||||
|
|
||||||
|
Developer_write_pair
|
||||||
|
Developer_write_fix
|
||||||
|
|||||||
245
doc/src/Developer_write_fix.rst
Normal file
245
doc/src/Developer_write_fix.rst
Normal file
@ -0,0 +1,245 @@
|
|||||||
|
Writing a new fix style
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
Writing fix styles is a flexible way of extending LAMMPS. Users can
|
||||||
|
implement many things using fixes. Some fix styles are only used
|
||||||
|
internally to support compute styles or pair styles:
|
||||||
|
|
||||||
|
- change particles attributes (positions, velocities, forces, etc.). Examples: ``FixNVE``, ``FixFreeze``.
|
||||||
|
- read or write data. Example: ``FixRestart``.
|
||||||
|
- adding or modifying properties due to geometry. Example: ``FixWall``.
|
||||||
|
- interacting with other subsystems or external code: Examples: ``FixTTM``, ``FixExternal``, ``FixMDI``
|
||||||
|
- saving information for analysis or future use (previous positions,
|
||||||
|
for instance). Examples: ``FixAveTime``, ``FixStoreState``.
|
||||||
|
|
||||||
|
All fixes are derived from the ``Fix`` base class and must have a
|
||||||
|
constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
|
||||||
|
|
||||||
|
Every fix must be registered in LAMMPS by writing the following lines
|
||||||
|
of code in the header before include guards:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
#ifdef FIX_CLASS
|
||||||
|
// clang-format off
|
||||||
|
FixStyle(print/vel,FixPrintVel);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
/* the definition of the FixPrintVel class comes here */
|
||||||
|
...
|
||||||
|
#endif
|
||||||
|
|
||||||
|
Where ``print/vel`` is the style name of your fix in the input script and
|
||||||
|
``FixPrintVel`` is the name of the class. The header file would be called
|
||||||
|
``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
|
||||||
|
These conventions allow LAMMPS to automatically integrate it into the
|
||||||
|
executable when compiling and associate your new fix class with the designated
|
||||||
|
keyword when it parses the input script.
|
||||||
|
|
||||||
|
Let's write a simple fix which will print the average velocity at the end
|
||||||
|
of each timestep. First of all, implement a constructor:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
|
||||||
|
: Fix(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
if (narg < 4) utils::missing_cmd_args(FLERR, "fix print/vel", error);
|
||||||
|
|
||||||
|
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||||
|
if (nevery <= 0)
|
||||||
|
error->all(FLERR,"Illegal fix print/vel nevery value: {}", nevery);
|
||||||
|
}
|
||||||
|
|
||||||
|
In the constructor you should parse the fix arguments which are
|
||||||
|
specified in the script. All fixes have pretty much the same syntax:
|
||||||
|
``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The first 3
|
||||||
|
parameters are parsed by Fix base class constructor, while ``<fix
|
||||||
|
arguments>`` should be parsed by you. In our case, we need to specify
|
||||||
|
how often we want to print an average velocity. For instance, once in 50
|
||||||
|
timesteps: ``fix 1 print/vel 50``. There is a special variable in the
|
||||||
|
Fix class called ``nevery`` which specifies how often the method
|
||||||
|
``end_of_step()`` is called. Thus all we need to do is just set it up.
|
||||||
|
|
||||||
|
The next method we need to implement is ``setmask()``:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
int FixPrintVel::setmask()
|
||||||
|
{
|
||||||
|
int mask = 0;
|
||||||
|
mask |= FixConst::END_OF_STEP;
|
||||||
|
return mask;
|
||||||
|
}
|
||||||
|
|
||||||
|
Here the we specify which methods of the fix should be called during
|
||||||
|
:doc:`execution of a timestep <Developer_flow>`. The constant
|
||||||
|
``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
|
||||||
|
important available methods that are called during a timestep.
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
void FixPrintVel::end_of_step()
|
||||||
|
{
|
||||||
|
// for add3, scale3
|
||||||
|
using namespace MathExtra;
|
||||||
|
|
||||||
|
double** v = atom->v;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double localAvgVel[4]; // 4th element for particles count
|
||||||
|
memset(localAvgVel, 0, 4 * sizeof(double));
|
||||||
|
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
||||||
|
add3(localAvgVel, v[particleInd], localAvgVel);
|
||||||
|
}
|
||||||
|
localAvgVel[3] = nlocal;
|
||||||
|
double globalAvgVel[4];
|
||||||
|
memset(globalAvgVel, 0, 4 * sizeof(double));
|
||||||
|
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
|
||||||
|
scale3(1.0 / globalAvgVel[3], globalAvgVel);
|
||||||
|
if ((comm->me == 0) && screen) {
|
||||||
|
fmt::print(screen,"{}, {}, {}\n",
|
||||||
|
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
In the code above, we use MathExtra routines defined in
|
||||||
|
``math_extra.h``. There are bunch of math functions to work with
|
||||||
|
arrays of doubles as with math vectors. It is also important to note
|
||||||
|
that LAMMPS code should always assume to be run in parallel and that
|
||||||
|
atom data is thus distributed across the MPI ranks. Thus you can
|
||||||
|
only process data from local atoms directly and need to use MPI library
|
||||||
|
calls to combine or exchange data. For serial execution, LAMMPS
|
||||||
|
comes bundled with the MPI STUBS library that contains the MPI library
|
||||||
|
function calls in dummy versions that only work for a single MPI rank.
|
||||||
|
|
||||||
|
In this code we use an instance of Atom class. This object is stored
|
||||||
|
in the Pointers class (see ``pointers.h``) which is the base class of
|
||||||
|
the Fix base class. This object contains references to various class
|
||||||
|
instances (the original instances are created and held by the LAMMPS
|
||||||
|
class) with all global information about the simulation system.
|
||||||
|
Data from the Pointers class is available to all classes inherited from
|
||||||
|
it using protected inheritance. Hence when you write you own class,
|
||||||
|
which is going to use LAMMPS data, don't forget to inherit from Pointers
|
||||||
|
or pass a Pointer to it to all functions that need access. When writing
|
||||||
|
fixes we inherit from class Fix which is inherited from Pointers so
|
||||||
|
there is no need to inherit from it directly.
|
||||||
|
|
||||||
|
The code above computes average velocity for all particles in the
|
||||||
|
simulation. Yet you have one unused parameter in fix call from the
|
||||||
|
script: ``group_name``. This parameter specifies the group of atoms
|
||||||
|
used in the fix. So we should compute average for all particles in the
|
||||||
|
simulation only if ``group_name == "all"``, but it can be any group.
|
||||||
|
The group membership information of an atom is contained in the *mask*
|
||||||
|
property of an atom and the bit corresponding to a given group is
|
||||||
|
stored in the groupbit variable which is defined in Fix base class:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; ++i) {
|
||||||
|
if (atom->mask[i] & groupbit) {
|
||||||
|
// Do all job here
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
Class Atom encapsulates atoms positions, velocities, forces, etc. Users
|
||||||
|
can access them using particle index. Note, that particle indexes are
|
||||||
|
usually changed every few timesteps because of neighbor list rebuilds
|
||||||
|
and spatial sorting (to improve cache efficiency).
|
||||||
|
|
||||||
|
Let us consider another Fix example: We want to have a fix which stores
|
||||||
|
atoms position from the previous time step in your fix. The local atoms
|
||||||
|
indexes may not be valid on the next iteration. In order to handle
|
||||||
|
this situation there are several methods which should be implemented:
|
||||||
|
|
||||||
|
- ``double memory_usage()``: return how much memory the fix uses (optional)
|
||||||
|
- ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
|
||||||
|
- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
|
||||||
|
information to j-th. Used when atom sorting is performed. if delflag is set
|
||||||
|
and atom j owns a body, move the body information to atom i.
|
||||||
|
- ``void set_arrays(int i)``: sets i-th particle related information to zero
|
||||||
|
|
||||||
|
Note, that if your class implements these methods, it must add calls of
|
||||||
|
add_callback and delete_callback to the constructor and destructor. Since we want
|
||||||
|
to store positions of atoms from the previous timestep, we need to add
|
||||||
|
``double** xold`` to the header file. Than add allocation code
|
||||||
|
to the constructor:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
|
||||||
|
{
|
||||||
|
//...
|
||||||
|
memory->create(xold, atom->nmax, 3, "FixSavePos:x");
|
||||||
|
atom->add_callback(0);
|
||||||
|
}
|
||||||
|
|
||||||
|
FixSavePos::~FixSavePos() {
|
||||||
|
atom->delete_callback(id, 0);
|
||||||
|
memory->destroy(xold);
|
||||||
|
}
|
||||||
|
|
||||||
|
Implement the aforementioned methods:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
double FixSavePos::memory_usage()
|
||||||
|
{
|
||||||
|
int nmax = atom->nmax;
|
||||||
|
double bytes = 0.0;
|
||||||
|
bytes += nmax * 3 * sizeof(double);
|
||||||
|
return bytes;
|
||||||
|
}
|
||||||
|
|
||||||
|
void FixSavePos::grow_arrays(int nmax)
|
||||||
|
{
|
||||||
|
memory->grow(xold, nmax, 3, "FixSavePos:xold");
|
||||||
|
}
|
||||||
|
|
||||||
|
void FixSavePos::copy_arrays(int i, int j, int delflag)
|
||||||
|
{
|
||||||
|
memcpy(xold[j], xold[i], sizeof(double) * 3);
|
||||||
|
}
|
||||||
|
|
||||||
|
void FixSavePos::set_arrays(int i)
|
||||||
|
{
|
||||||
|
memset(xold[i], 0, sizeof(double) * 3);
|
||||||
|
}
|
||||||
|
|
||||||
|
int FixSavePos::pack_exchange(int i, double *buf)
|
||||||
|
{
|
||||||
|
int m = 0;
|
||||||
|
buf[m++] = xold[i][0];
|
||||||
|
buf[m++] = xold[i][1];
|
||||||
|
buf[m++] = xold[i][2];
|
||||||
|
|
||||||
|
return m;
|
||||||
|
}
|
||||||
|
|
||||||
|
int FixSavePos::unpack_exchange(int nlocal, double *buf)
|
||||||
|
{
|
||||||
|
int m = 0;
|
||||||
|
xold[nlocal][0] = buf[m++];
|
||||||
|
xold[nlocal][1] = buf[m++];
|
||||||
|
xold[nlocal][2] = buf[m++];
|
||||||
|
|
||||||
|
return m;
|
||||||
|
}
|
||||||
|
|
||||||
|
Now, a little bit about memory allocation. We use the Memory class which
|
||||||
|
is just a bunch of template functions for allocating 1D and 2D
|
||||||
|
arrays. So you need to add include ``memory.h`` to have access to them.
|
||||||
|
|
||||||
|
Finally, if you need to write/read some global information used in
|
||||||
|
your fix to the restart file, you might do it by setting flag
|
||||||
|
``restart_global = 1`` in the constructor and implementing methods void
|
||||||
|
``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
|
||||||
|
If, in addition, you want to write the per-atom property to restart
|
||||||
|
files additional settings and functions are needed:
|
||||||
|
|
||||||
|
- a fix flag indicating this needs to be set ``restart_peratom = 1;``
|
||||||
|
- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
|
||||||
|
a second time with the final argument set to 1 instead of 0 (indicating
|
||||||
|
restart processing instead of per-atom data memory management).
|
||||||
|
- the functions ``void pack_restart(int i, double *buf)`` and
|
||||||
|
``void unpack_restart(int nlocal, int nth)`` need to be implemented
|
||||||
|
|
||||||
1354
doc/src/Developer_write_pair.rst
Normal file
1354
doc/src/Developer_write_pair.rst
Normal file
File diff suppressed because it is too large
Load Diff
@ -70,6 +70,7 @@ Force fields howto
|
|||||||
Howto_amoeba
|
Howto_amoeba
|
||||||
Howto_tip3p
|
Howto_tip3p
|
||||||
Howto_tip4p
|
Howto_tip4p
|
||||||
|
Howto_tip5p
|
||||||
Howto_spc
|
Howto_spc
|
||||||
|
|
||||||
Packages howto
|
Packages howto
|
||||||
|
|||||||
@ -43,6 +43,15 @@ The fix style *freeze* zeroes both the force and torque of frozen
|
|||||||
atoms, and should be used for granular system instead of the fix style
|
atoms, and should be used for granular system instead of the fix style
|
||||||
*setforce*\ .
|
*setforce*\ .
|
||||||
|
|
||||||
|
To model heat conduction, one must add the temperature and heatflow
|
||||||
|
atom variables with:
|
||||||
|
* :doc:`fix property/atom <fix_property_atom>`
|
||||||
|
a temperature integration fix
|
||||||
|
* :doc:`fix heat/flow <fix_heat_flow>`
|
||||||
|
and a heat conduction option defined in both
|
||||||
|
* :doc:`pair_style granular <pair_granular>`
|
||||||
|
* :doc:`fix wall/gran <fix_wall_gran>`
|
||||||
|
|
||||||
For computational efficiency, you can eliminate needless pairwise
|
For computational efficiency, you can eliminate needless pairwise
|
||||||
computations between frozen atoms by using this command:
|
computations between frozen atoms by using this command:
|
||||||
|
|
||||||
@ -55,3 +64,6 @@ computations between frozen atoms by using this command:
|
|||||||
will be the same as in 3d. If you wish to model granular particles in
|
will be the same as in 3d. If you wish to model granular particles in
|
||||||
2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
|
2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
|
||||||
doc page, where 2d simulations are discussed.
|
doc page, where 2d simulations are discussed.
|
||||||
|
|
||||||
|
To add custom granular contact models, see the
|
||||||
|
:doc:`modifying granular sub-models page <Modify_gran_sub_mod>`.
|
||||||
|
|||||||
@ -63,22 +63,29 @@ The package also provides a :doc:`mdi plugin <mdi>` command, which
|
|||||||
enables LAMMPS to operate as an MDI driver and load an MDI engine as a
|
enables LAMMPS to operate as an MDI driver and load an MDI engine as a
|
||||||
plugin library.
|
plugin library.
|
||||||
|
|
||||||
The package furthermore includes a `fix mdi/qm <fix_mdi_qm>` command, in
|
The package furthermore includes a :doc:`fix mdi/qm <fix_mdi_qm>`
|
||||||
which LAMMPS operates as an MDI driver in conjunction with a quantum
|
command, in which LAMMPS operates as an MDI driver in conjunction with a
|
||||||
mechanics code as an MDI engine. The post_force() method of the
|
quantum mechanics code as an MDI engine. The post_force() method of the
|
||||||
``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to another
|
``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to
|
||||||
code. This command can be used to couple to an MDI engine, which is
|
another code. This command can be used to couple to an MDI engine,
|
||||||
either a stand-alone code or a plugin library.
|
which is either a stand-alone code or a plugin library.
|
||||||
|
|
||||||
As explained in the `fix mdi/qm <fix_mdi_qm>` command documentation, it
|
As explained in the :doc:`fix mdi/qm <fix_mdi_qm>` command
|
||||||
can be used to perform *ab initio* MD simulations or energy
|
documentation, it can be used to perform *ab initio* MD simulations or
|
||||||
minimizations, or to evaluate the quantum energy and forces for a series
|
energy minimizations, or to evaluate the quantum energy and forces for a
|
||||||
of independent systems. The ``examples/mdi`` directory has example
|
series of independent systems. The ``examples/mdi`` directory has
|
||||||
input scripts for all of these use cases.
|
example input scripts for all of these use cases.
|
||||||
|
|
||||||
|
The package also has a :doc:`fix mdi/qmmm <fix_mdi_qmmm>` command in
|
||||||
|
which LAMMPS operates as an MDI driver in conjunction with a quantum
|
||||||
|
mechanics code as an MDI engine to perform QM/MM simulations. The
|
||||||
|
LAMMPS input script partitions the system into QM and MM (molecular
|
||||||
|
mechanics) atoms. As described below the ``examples/QUANTUM`` directory
|
||||||
|
has examples for coupling to 3 different quantum codes in this manner.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The examples/mdi directory contains Python scripts and LAMMPS input
|
The ``examples/mdi`` directory contains Python scripts and LAMMPS input
|
||||||
script which use LAMMPS as either an MDI driver or engine, or both.
|
script which use LAMMPS as either an MDI driver or engine, or both.
|
||||||
Currently, 5 example use cases are provided:
|
Currently, 5 example use cases are provided:
|
||||||
|
|
||||||
@ -119,45 +126,26 @@ as a plugin library.
|
|||||||
|
|
||||||
-------------
|
-------------
|
||||||
|
|
||||||
Currently, there are at least two quantum DFT codes which have direct MDI
|
As of March 2023, these are quantum codes with MDI support provided via
|
||||||
|
Python wrapper scripts included in the LAMMPS distribution. These can
|
||||||
|
be used with the fix mdi/qm and fix mdi/qmmm commands to perform QM
|
||||||
|
calculations of an entire system (e.g. AIMD) or QM/MM simulations. See
|
||||||
|
the ``examples/QUANTUM`` sub-directories for more details:
|
||||||
|
|
||||||
|
* LATTE - AIMD only
|
||||||
|
* PySCF - QM/MM only
|
||||||
|
* NWChem - AIMD or QM/MM
|
||||||
|
|
||||||
|
There are also at least two quantum codes which have direct MDI
|
||||||
support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
|
support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
|
||||||
and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also several
|
and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also
|
||||||
QM codes which have indirect support through QCEngine or i-PI. The
|
several QM codes which have indirect support through QCEngine or i-PI.
|
||||||
former means they require a wrapper program (QCEngine) with MDI support
|
The former means they require a wrapper program (QCEngine) with MDI
|
||||||
which writes/read files to pass data to the quantum code itself. The
|
support which writes/read files to pass data to the quantum code
|
||||||
list of QCEngine-supported and i-PI-supported quantum codes is on the
|
itself. The list of QCEngine-supported and i-PI-supported quantum
|
||||||
`MDI webpage
|
codes is on the `MDI webpage
|
||||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
||||||
|
|
||||||
Here is how to build QE as a stand-alone ``pw.x`` file which can be
|
These direct- and indirect-support codes should be usable for full
|
||||||
used in stand-alone mode:
|
system calculations (e.g. AIMD). Whether they support QM/MM models
|
||||||
|
depends on the individual QM code.
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
|
|
||||||
build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
|
|
||||||
|
|
||||||
Here is how to build QE as a shared library which can be used in plugin mode,
|
|
||||||
which results in a ``libqemdi.so`` file in ``<base_path>/q-e/MDI/src``:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
|
|
||||||
cd <base_path>/q-e
|
|
||||||
./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
|
|
||||||
make -j 4 mdi
|
|
||||||
|
|
||||||
INQ cannot be built as a stand-alone code; it is by design a library.
|
|
||||||
Here is how to build INQ as a shared library which can be used in
|
|
||||||
plugin mode, which results in a ``libinqmdi.so`` file in
|
|
||||||
``<base_path>/inq/build/examples``:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
|
|
||||||
cd <base_path>/inq
|
|
||||||
mkdir -p build
|
|
||||||
cd build
|
|
||||||
../configure --prefix=<install_path>/install
|
|
||||||
make -j 4
|
|
||||||
make install
|
|
||||||
|
|||||||
@ -20,7 +20,6 @@ atoms and the water molecule to run a rigid SPC model.
|
|||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
||||||
| :math:`r_0` of OH bond = 1.0
|
| :math:`r_0` of OH bond = 1.0
|
||||||
| :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
|
| :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
|
||||||
|
|
|
||||||
|
|
||||||
Note that as originally proposed, the SPC model was run with a 9
|
Note that as originally proposed, the SPC model was run with a 9
|
||||||
Angstrom cutoff for both LJ and Coulomb terms. It can also be used
|
Angstrom cutoff for both LJ and Coulomb terms. It can also be used
|
||||||
@ -33,16 +32,123 @@ the partial charge assignments change:
|
|||||||
|
|
||||||
| O charge = -0.8476
|
| O charge = -0.8476
|
||||||
| H charge = 0.4238
|
| H charge = 0.4238
|
||||||
|
|
|
||||||
|
|
||||||
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
|
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
|
||||||
the SPC and SPC/E models.
|
the SPC and SPC/E models.
|
||||||
|
|
||||||
|
Below is the code for a LAMMPS input file and a molecule file
|
||||||
|
(``spce.mol``) of SPC/E water for use with the :doc:`molecule command
|
||||||
|
<molecule>` demonstrating how to set up a small bulk water system for
|
||||||
|
SPC/E with rigid bonds.
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 &
|
||||||
|
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
|
mass 2 1.008
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/cut 10.0
|
||||||
|
pair_coeff 1 1 0.1553 3.166
|
||||||
|
pair_coeff 1 2 0.0 1.0
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
|
||||||
|
bond_style zero
|
||||||
|
bond_coeff 1 1.0
|
||||||
|
|
||||||
|
angle_style zero
|
||||||
|
angle_coeff 1 109.47
|
||||||
|
|
||||||
|
molecule water spce.mol
|
||||||
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
|
||||||
|
timestep 1.0
|
||||||
|
fix rigid all shake 0.0001 10 10000 b 1 a 1
|
||||||
|
minimize 0.0 0.0 1000 10000
|
||||||
|
run 0 post no
|
||||||
|
reset_timestep 0
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
fix integrate all nvt temp 300.0 300.0 1.0
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal density pe ke
|
||||||
|
thermo 1000
|
||||||
|
run 20000 upto
|
||||||
|
write_data tip4p.data nocoeff
|
||||||
|
|
||||||
|
.. _spce_molecule:
|
||||||
|
.. code-block::
|
||||||
|
|
||||||
|
# Water molecule. SPC/E geometry
|
||||||
|
|
||||||
|
3 atoms
|
||||||
|
2 bonds
|
||||||
|
1 angles
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 0.00000 -0.06461 0.00000
|
||||||
|
2 0.81649 0.51275 0.00000
|
||||||
|
3 -0.81649 0.51275 0.00000
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1 # O
|
||||||
|
2 2 # H
|
||||||
|
3 2 # H
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 -0.8476
|
||||||
|
2 0.4238
|
||||||
|
3 0.4238
|
||||||
|
|
||||||
|
Bonds
|
||||||
|
|
||||||
|
1 1 1 2
|
||||||
|
2 1 1 3
|
||||||
|
|
||||||
|
Angles
|
||||||
|
|
||||||
|
1 1 2 1 3
|
||||||
|
|
||||||
|
Shake Flags
|
||||||
|
|
||||||
|
1 1
|
||||||
|
2 1
|
||||||
|
3 1
|
||||||
|
|
||||||
|
Shake Atoms
|
||||||
|
|
||||||
|
1 1 2 3
|
||||||
|
2 1 2 3
|
||||||
|
3 1 2 3
|
||||||
|
|
||||||
|
Shake Bond Types
|
||||||
|
|
||||||
|
1 1 1 1
|
||||||
|
2 1 1 1
|
||||||
|
3 1 1 1
|
||||||
|
|
||||||
|
Special Bond Counts
|
||||||
|
|
||||||
|
1 2 0 0
|
||||||
|
2 1 1 0
|
||||||
|
3 1 1 0
|
||||||
|
|
||||||
|
Special Bonds
|
||||||
|
|
||||||
|
1 2 3
|
||||||
|
2 1 3
|
||||||
|
3 1 2
|
||||||
|
|
||||||
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _howto-Berendsen:
|
.. _howto-Berendsen:
|
||||||
|
|
||||||
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
|
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
|
||||||
6269-6271 (1987).
|
|
||||||
|
|||||||
@ -1,53 +1,211 @@
|
|||||||
TIP3P water model
|
TIP3P water model
|
||||||
=================
|
=================
|
||||||
|
|
||||||
The TIP3P water model as implemented in CHARMM
|
The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
|
||||||
:ref:`(MacKerell) <howto-tip3p>` specifies a 3-site rigid water molecule with
|
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
|
||||||
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
|
Lennard-Jones parameters assigned to each of the 3 atoms.
|
||||||
In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
|
|
||||||
the two O-H bonds and the H-O-H angle rigid. A bond style of
|
|
||||||
*harmonic* and an angle style of *harmonic* or *charmm* should also be
|
|
||||||
used.
|
|
||||||
|
|
||||||
These are the additional parameters (in real units) to set for O and H
|
A suitable pair style with cutoff Coulomb would be:
|
||||||
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
|
|
||||||
cutoff. The K values can be used if a flexible TIP3P model (without
|
|
||||||
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
|
|
||||||
set to 0.0, it corresponds to the original 1983 TIP3P model
|
|
||||||
:ref:`(Jorgensen) <Jorgensen1>`.
|
|
||||||
|
|
||||||
| O mass = 15.9994
|
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
|
||||||
| H mass = 1.008
|
|
||||||
| O charge = -0.834
|
|
||||||
| H charge = 0.417
|
|
||||||
| LJ :math:`\epsilon` of OO = 0.1521
|
|
||||||
| LJ :math:`\sigma` of OO = 3.1507
|
|
||||||
| LJ :math:`\epsilon` of HH = 0.0460
|
|
||||||
| LJ :math:`\sigma` of HH = 0.4000
|
|
||||||
| LJ :math:`\epsilon` of OH = 0.0836
|
|
||||||
| LJ :math:`\sigma` of OH = 1.7753
|
|
||||||
| K of OH bond = 450
|
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
|
||||||
| K of HOH angle = 55
|
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
|
||||||
|
|
|
||||||
|
|
||||||
These are the parameters to use for TIP3P with a long-range Coulomb
|
or these commands for a long-range Coulomb model:
|
||||||
solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
|
|
||||||
details:
|
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
|
||||||
|
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
|
||||||
|
* :doc:`kspace_style pppm <kspace_style>`
|
||||||
|
* :doc:`kspace_style pppm/disp <kspace_style>`
|
||||||
|
|
||||||
|
In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
|
||||||
|
used to hold the two O-H bonds and the H-O-H angle rigid. A bond style
|
||||||
|
of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
|
||||||
|
<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
|
||||||
|
In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
|
||||||
|
style :doc:`zero <angle_zero>` can be used.
|
||||||
|
|
||||||
|
The table below lists the force field parameters (in real :doc:`units
|
||||||
|
<units>`) to for the water molecule atoms to run a rigid or flexible
|
||||||
|
TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model
|
||||||
|
:ref:`(Jorgensen) <Jorgensen1>`, or a TIP3P model with parameters
|
||||||
|
optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
|
||||||
|
:ref:`(Price) <Price1>`. The K values can be used if a flexible TIP3P
|
||||||
|
model (without fix shake) is desired, for rigid bonds/angles they are
|
||||||
|
ignored.
|
||||||
|
|
||||||
|
.. list-table::
|
||||||
|
:header-rows: 1
|
||||||
|
:widths: auto
|
||||||
|
|
||||||
|
* - Parameter
|
||||||
|
- TIP3P-CHARMM
|
||||||
|
- TIP3P (original)
|
||||||
|
- TIP3P (Ewald)
|
||||||
|
* - O mass (amu)
|
||||||
|
- 15.9994
|
||||||
|
- 15.9994
|
||||||
|
- 15.9994
|
||||||
|
* - H mass (amu)
|
||||||
|
- 1.008
|
||||||
|
- 1.008
|
||||||
|
- 1.008
|
||||||
|
* - O charge (:math:`e`)
|
||||||
|
- -0.834
|
||||||
|
- -0.834
|
||||||
|
- -0.834
|
||||||
|
* - H charge (:math:`e`)
|
||||||
|
- 0.417
|
||||||
|
- 0.417
|
||||||
|
- 0.417
|
||||||
|
* - LJ :math:`\epsilon` of OO (kcal/mole)
|
||||||
|
- 0.1521
|
||||||
|
- 0.1521
|
||||||
|
- 0.1020
|
||||||
|
* - LJ :math:`\sigma` of OO (:math:`\AA`)
|
||||||
|
- 3.1507
|
||||||
|
- 3.1507
|
||||||
|
- 3.188
|
||||||
|
* - LJ :math:`\epsilon` of HH (kcal/mole)
|
||||||
|
- 0.0460
|
||||||
|
- 0.0
|
||||||
|
- 0.0
|
||||||
|
* - LJ :math:`\sigma` of HH (:math:`\AA`)
|
||||||
|
- 0.4
|
||||||
|
- 1.0
|
||||||
|
- 1.0
|
||||||
|
* - LJ :math:`\epsilon` of OH (kcal/mole)
|
||||||
|
- 0.0836
|
||||||
|
- 0.0
|
||||||
|
- 0.0
|
||||||
|
* - LJ :math:`\sigma` of OH (:math:`\AA`)
|
||||||
|
- 1.7753
|
||||||
|
- 1.0
|
||||||
|
- 1.0
|
||||||
|
* - K of OH bond (kcal/mole/:math:`\AA^2`)
|
||||||
|
- 450
|
||||||
|
- 450
|
||||||
|
- 450
|
||||||
|
* - :math:`r_0` of OH bond (:math:`\AA`)
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
* - K of HOH angle (kcal/mole)
|
||||||
|
- 55.0
|
||||||
|
- 55.0
|
||||||
|
- 55.0
|
||||||
|
* - :math:`\theta_0` of HOH angle
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
|
||||||
|
Below is the code for a LAMMPS input file and a molecule file
|
||||||
|
(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
|
||||||
|
<molecule>` demonstrating how to set up a small bulk water system for
|
||||||
|
TIP3P with rigid bonds.
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 &
|
||||||
|
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
|
mass 2 1.008
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/cut 8.0
|
||||||
|
pair_coeff 1 1 0.1521 3.1507
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
|
||||||
|
bond_style zero
|
||||||
|
bond_coeff 1 0.9574
|
||||||
|
|
||||||
|
angle_style zero
|
||||||
|
angle_coeff 1 104.52
|
||||||
|
|
||||||
|
molecule water tip3p.mol
|
||||||
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
|
||||||
|
fix rigid all shake 0.001 10 10000 b 1 a 1
|
||||||
|
minimize 0.0 0.0 1000 10000
|
||||||
|
run 0 post no
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
fix integrate all nvt temp 300 300 1.0
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal pe
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
run 20000
|
||||||
|
write_data tip3p.data nocoeff
|
||||||
|
|
||||||
|
.. _tip3p_molecule:
|
||||||
|
.. code-block::
|
||||||
|
|
||||||
|
# Water molecule. TIP3P geometry
|
||||||
|
|
||||||
|
3 atoms
|
||||||
|
2 bonds
|
||||||
|
1 angles
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 0.00000 -0.06556 0.00000
|
||||||
|
2 0.75695 0.52032 0.00000
|
||||||
|
3 -0.75695 0.52032 0.00000
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1 # O
|
||||||
|
2 2 # H
|
||||||
|
3 2 # H
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 -0.834
|
||||||
|
2 0.417
|
||||||
|
3 0.417
|
||||||
|
|
||||||
|
Bonds
|
||||||
|
|
||||||
|
1 1 1 2
|
||||||
|
2 1 1 3
|
||||||
|
|
||||||
|
Angles
|
||||||
|
|
||||||
|
1 1 2 1 3
|
||||||
|
|
||||||
|
Shake Flags
|
||||||
|
|
||||||
|
1 1
|
||||||
|
2 1
|
||||||
|
3 1
|
||||||
|
|
||||||
|
Shake Atoms
|
||||||
|
|
||||||
|
1 1 2 3
|
||||||
|
2 1 2 3
|
||||||
|
3 1 2 3
|
||||||
|
|
||||||
|
Shake Bond Types
|
||||||
|
|
||||||
|
1 1 1 1
|
||||||
|
2 1 1 1
|
||||||
|
3 1 1 1
|
||||||
|
|
||||||
|
Special Bond Counts
|
||||||
|
|
||||||
|
1 2 0 0
|
||||||
|
2 1 1 0
|
||||||
|
3 1 1 0
|
||||||
|
|
||||||
|
Special Bonds
|
||||||
|
|
||||||
|
1 2 3
|
||||||
|
2 1 3
|
||||||
|
3 1 2
|
||||||
|
|
||||||
| O mass = 15.9994
|
|
||||||
| H mass = 1.008
|
|
||||||
| O charge = -0.830
|
|
||||||
| H charge = 0.415
|
|
||||||
| LJ :math:`\epsilon` of OO = 0.102
|
|
||||||
| LJ :math:`\sigma` of OO = 3.188
|
|
||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
|
||||||
| K of OH bond = 450
|
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
|
||||||
| K of HOH angle = 55
|
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
|
||||||
|
|
|
||||||
|
|
||||||
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
||||||
|
|
||||||
|
|||||||
@ -2,19 +2,33 @@ TIP4P water model
|
|||||||
=================
|
=================
|
||||||
|
|
||||||
The four-point TIP4P rigid water model extends the traditional
|
The four-point TIP4P rigid water model extends the traditional
|
||||||
three-point TIP3P model by adding an additional site, usually
|
:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
|
||||||
massless, where the charge associated with the oxygen atom is placed.
|
site M, usually massless, where the charge associated with the oxygen
|
||||||
This site M is located at a fixed distance away from the oxygen along
|
atom is placed. This site M is located at a fixed distance away from
|
||||||
the bisector of the HOH bond angle. A bond style of *harmonic* and an
|
the oxygen along the bisector of the HOH bond angle. A bond style of
|
||||||
angle style of *harmonic* or *charmm* should also be used.
|
:doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
|
||||||
|
<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
|
||||||
|
In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
|
||||||
|
style :doc:`zero <angle_zero>` can be used.
|
||||||
|
|
||||||
A TIP4P model is run with LAMMPS using either these commands
|
There are two ways to implement TIP4P water in LAMMPS:
|
||||||
for a cutoff model:
|
|
||||||
|
#. Use a specially written pair style that uses the :ref:`TIP3P geometry
|
||||||
|
<tip3p_molecule>` without the point M. The point M location is then
|
||||||
|
implicitly derived from the other atoms or each water molecule and
|
||||||
|
used during the force computation. The forces on M are then
|
||||||
|
projected on the oxygen and the two hydrogen atoms. This is
|
||||||
|
computationally very efficient, but the charge distribution in space
|
||||||
|
is only correct within the tip4p labeled styles. So all other
|
||||||
|
computations using charges will "see" the negative charge incorrectly
|
||||||
|
on the oxygen atom.
|
||||||
|
|
||||||
|
This can be done with the following pair styles for Coulomb with a cutoff:
|
||||||
|
|
||||||
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
|
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
|
||||||
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
|
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
|
||||||
|
|
||||||
or these commands for a long-range model:
|
or these commands for a long-range Coulomb treatment:
|
||||||
|
|
||||||
* :doc:`pair_style tip4p/long <pair_coul>`
|
* :doc:`pair_style tip4p/long <pair_coul>`
|
||||||
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
|
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
|
||||||
@ -31,71 +45,95 @@ parameter sets listed below are all for rigid TIP4P model variants and
|
|||||||
thus the bond and angle force constants are not used and can be set to
|
thus the bond and angle force constants are not used and can be set to
|
||||||
any legal value; only equilibrium length and angle are used.
|
any legal value; only equilibrium length and angle are used.
|
||||||
|
|
||||||
These are the additional parameters (in real units) to set for O and H
|
#. Use an :ref:`explicit 4 point TIP4P geometry <tip4p_molecule>` where
|
||||||
atoms and the water molecule to run a rigid TIP4P model with a cutoff
|
the oxygen atom carries no charge and the M point no Lennard-Jones
|
||||||
:ref:`(Jorgensen) <Jorgensen5>`. Note that the OM distance is specified in
|
interactions. Since :doc:`fix shake <fix_shake>` or :doc:`fix rattle
|
||||||
the :doc:`pair_style <pair_style>` command, not as part of the pair
|
<fix_shake>` may not be applied to this kind of geometry, :doc:`fix
|
||||||
coefficients.
|
rigid or fix rigid/small <fix_rigid>` or its thermostatted variants
|
||||||
|
are required to maintain a rigid geometry. This avoids some of the
|
||||||
|
issues with respect to analysis and non-tip4p styles, but it is a
|
||||||
|
more costly force computation (more atoms in the same volume and thus
|
||||||
|
more neighbors in the neighbor lists) and requires a much shorter
|
||||||
|
timestep for stable integration of the rigid body motion. Since no
|
||||||
|
bonds or angles are required, they do not need to be defined and atom
|
||||||
|
style charge would be sufficient for a bulk TIP4P water system. In
|
||||||
|
order to avoid that LAMMPS produces an error due to the massless M
|
||||||
|
site a tiny non-zero mass needs to be assigned.
|
||||||
|
|
||||||
| O mass = 15.9994
|
The table below lists the force field parameters (in real :doc:`units
|
||||||
| H mass = 1.008
|
<units>`) to for a selection of popular variants of the TIP4P model.
|
||||||
| O charge = -1.040
|
There is the rigid TIP4P model with a cutoff :ref:`(Jorgensen)
|
||||||
| H charge = 0.520
|
<Jorgensen5>`, the TIP4/Ice model :ref:`(Abascal1) <Abascal1>`, the
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
parameters adjusted for use with a long-range Coulombic solver
|
||||||
| OM distance = 0.15
|
(e.g. Ewald or PPPM in LAMMPS). Note that for implicit TIP4P models the
|
||||||
| LJ :math:`\epsilon` of O-O = 0.1550
|
OM distance is specified in the :doc:`pair_style <pair_style>` command,
|
||||||
| LJ :math:`\sigma` of O-O = 3.1536
|
not as part of the pair coefficients.
|
||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
|
||||||
| Coulomb cutoff = 8.5
|
|
||||||
|
|
|
||||||
|
|
||||||
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
|
.. list-table::
|
||||||
https://doi.org/10.1063/1.1931662) these values can be used:
|
:header-rows: 1
|
||||||
|
:widths: auto
|
||||||
|
|
||||||
| O mass = 15.9994
|
* - Parameter
|
||||||
| H mass = 1.008
|
- TIP4P (original)
|
||||||
| O charge = -1.1794
|
- TIP4P/Ice
|
||||||
| H charge = 0.5897
|
- TIP4P/2005
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
- TIP4P (Ewald)
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
* - O mass (amu)
|
||||||
| OM distance = 0.1577
|
- 15.9994
|
||||||
| LJ :math:`\epsilon` of O-O = 0.21084
|
- 15.9994
|
||||||
| LJ :math:`\sigma` of O-O = 3.1668
|
- 15.9994
|
||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
- 15.9994
|
||||||
| Coulomb cutoff = 8.5
|
* - H mass (amu)
|
||||||
|
|
- 1.008
|
||||||
|
- 1.008
|
||||||
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
|
- 1.008
|
||||||
https://doi.org/10.1063/1.2121687), these values can be used:
|
- 1.008
|
||||||
|
* - O or M charge (:math:`e`)
|
||||||
| O mass = 15.9994
|
- -1.040
|
||||||
| H mass = 1.008
|
- -1.1794
|
||||||
| O charge = -1.1128
|
- -1.1128
|
||||||
| H charge = 0.5564
|
- -1.04844
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
* - H charge (:math:`e`)
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
- 0.520
|
||||||
| OM distance = 0.1546
|
- 0.5897
|
||||||
| LJ :math:`\epsilon` of O-O = 0.1852
|
- 0.5564
|
||||||
| LJ :math:`\sigma` of O-O = 3.1589
|
- 0.52422
|
||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
* - LJ :math:`\epsilon` of OO (kcal/mole)
|
||||||
| Coulomb cutoff = 8.5
|
- 0.1550
|
||||||
|
|
- 0.1577
|
||||||
|
- 0.1852
|
||||||
These are the parameters to use for TIP4P with a long-range Coulombic
|
- 0.16275
|
||||||
solver (e.g. Ewald or PPPM in LAMMPS):
|
* - LJ :math:`\sigma` of OO (:math:`\AA`)
|
||||||
|
- 3.1536
|
||||||
| O mass = 15.9994
|
- 3.1668
|
||||||
| H mass = 1.008
|
- 3.1589
|
||||||
| O charge = -1.0484
|
- 3.16435
|
||||||
| H charge = 0.5242
|
* - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
|
||||||
| :math:`r_0` of OH bond = 0.9572
|
- 0.0
|
||||||
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
- 0.0
|
||||||
| OM distance = 0.1250
|
- 0.0
|
||||||
| LJ :math:`\epsilon` of O-O = 0.16275
|
- 0.0
|
||||||
| LJ :math:`\sigma` of O-O = 3.16435
|
* - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
|
||||||
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
- 1.0
|
||||||
|
|
- 1.0
|
||||||
|
- 1.0
|
||||||
|
- 1.0
|
||||||
|
* - :math:`r_0` of OH bond (:math:`\AA`)
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
* - :math:`\theta_0` of HOH angle
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
* - OM distance (:math:`\AA`)
|
||||||
|
- 0.15
|
||||||
|
- 0.1577
|
||||||
|
- 0.1546
|
||||||
|
- 0.1250
|
||||||
|
|
||||||
Note that the when using the TIP4P pair style, the neighbor list cutoff
|
Note that the when using the TIP4P pair style, the neighbor list cutoff
|
||||||
for Coulomb interactions is effectively extended by a distance 2 \* (OM
|
for Coulomb interactions is effectively extended by a distance 2 \* (OM
|
||||||
@ -108,6 +146,117 @@ trade-off for your model. The OM distance and the LJ and Coulombic
|
|||||||
cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
|
cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
|
||||||
<pair_lj_cut_tip4p>` command.
|
<pair_lj_cut_tip4p>` command.
|
||||||
|
|
||||||
|
Below is the code for a LAMMPS input file using the implicit method and
|
||||||
|
the :ref:`TIP3P molecule file <tip3p_molecule>`. Because the TIP4P
|
||||||
|
charges are different from TIP3P they need to be reset (or the molecule
|
||||||
|
file changed):
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 &
|
||||||
|
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
|
mass 2 1.008
|
||||||
|
|
||||||
|
pair_style lj/cut/tip4p/cut 1 2 1 1 0.15 8.0
|
||||||
|
pair_coeff 1 1 0.1550 3.1536
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
|
||||||
|
bond_style zero
|
||||||
|
bond_coeff 1 0.9574
|
||||||
|
|
||||||
|
angle_style zero
|
||||||
|
angle_coeff 1 104.52
|
||||||
|
|
||||||
|
molecule water tip3p.mol # this uses the TIP3P geometry
|
||||||
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
# must change charges for TIP4P
|
||||||
|
set type 1 charge -1.040
|
||||||
|
set type 2 charge 0.520
|
||||||
|
|
||||||
|
fix rigid all shake 0.001 10 10000 b 1 a 1
|
||||||
|
minimize 0.0 0.0 1000 10000
|
||||||
|
run 0 post no
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
fix integrate all nvt temp 300 300 1.0
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal pe
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
run 20000
|
||||||
|
write_data tip3p.data nocoeff
|
||||||
|
|
||||||
|
Below is the code for a LAMMPS input file using the explicit method and
|
||||||
|
a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small
|
||||||
|
<fix_rigid>` no bonds need to be defined and thus no extra storage needs
|
||||||
|
to be reserved for them, but we need to switch to atom style full or use
|
||||||
|
:doc:`fix property/atom mol <fix_property_atom>` so that fix
|
||||||
|
rigid/nvt/small can identify rigid bodies by their molecule ID:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
create_box 3 box
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
|
mass 2 1.008
|
||||||
|
mass 3 1.0e-100
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/cut 8.0
|
||||||
|
pair_coeff 1 1 0.1550 3.1536
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
pair_coeff 3 3 0.0 1.0
|
||||||
|
|
||||||
|
fix mol all property/atom mol
|
||||||
|
molecule water tip4p.mol
|
||||||
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
|
||||||
|
timestep 0.1
|
||||||
|
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal density pe ke
|
||||||
|
thermo 1000
|
||||||
|
run 20000
|
||||||
|
write_data tip4p.data nocoeff
|
||||||
|
|
||||||
|
.. _tip4p_molecule:
|
||||||
|
.. code-block::
|
||||||
|
|
||||||
|
# Water molecule. Explicit TIP4P geometry for use with fix rigid
|
||||||
|
|
||||||
|
4 atoms
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 0.00000 -0.06556 0.00000
|
||||||
|
2 0.75695 0.52032 0.00000
|
||||||
|
3 -0.75695 0.52032 0.00000
|
||||||
|
4 0.00000 0.08444 0.00000
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1 # O
|
||||||
|
2 2 # H
|
||||||
|
3 2 # H
|
||||||
|
4 3 # M
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 0.000
|
||||||
|
2 0.520
|
||||||
|
3 0.520
|
||||||
|
4 -1.040
|
||||||
|
|
||||||
|
|
||||||
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
@ -116,3 +265,13 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
|
|||||||
|
|
||||||
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||||
Phys, 79, 926 (1983).
|
Phys, 79, 926 (1983).
|
||||||
|
|
||||||
|
.. _Abascal1:
|
||||||
|
|
||||||
|
**(Abascal1)** Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
|
||||||
|
https://doi.org/10.1063/1.1931662
|
||||||
|
|
||||||
|
.. _Abascal2:
|
||||||
|
|
||||||
|
**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
|
||||||
|
https://doi.org/10.1063/1.2121687
|
||||||
|
|||||||
161
doc/src/Howto_tip5p.rst
Normal file
161
doc/src/Howto_tip5p.rst
Normal file
@ -0,0 +1,161 @@
|
|||||||
|
TIP5P water model
|
||||||
|
=================
|
||||||
|
|
||||||
|
The five-point TIP5P rigid water model extends the :doc:`three-point
|
||||||
|
TIP3P model <Howto_tip3p>` by adding two additional sites L, usually
|
||||||
|
massless, where the charge associated with the oxygen atom is placed.
|
||||||
|
These sites L are located at a fixed distance away from the oxygen atom,
|
||||||
|
forming a tetrahedral angle that is rotated by 90 degrees from the HOH
|
||||||
|
plane. Those sites thus somewhat approximate lone pairs of the oxygen
|
||||||
|
and consequently improve the water structure to become even more
|
||||||
|
"tetrahedral" in comparison to the :doc:`four-point TIP4P model
|
||||||
|
<Howto_tip4p>`.
|
||||||
|
|
||||||
|
A suitable pair style with cutoff Coulomb would be:
|
||||||
|
|
||||||
|
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
|
||||||
|
|
||||||
|
or these commands for a long-range model:
|
||||||
|
|
||||||
|
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
|
||||||
|
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
|
||||||
|
* :doc:`kspace_style pppm <kspace_style>`
|
||||||
|
* :doc:`kspace_style pppm/disp <kspace_style>`
|
||||||
|
|
||||||
|
A TIP5P model *must* be run using a :doc:`rigid fix <fix_rigid>` since
|
||||||
|
there is no other option to keep this kind of structure rigid in LAMMPS.
|
||||||
|
In order to avoid that LAMMPS produces an error due to the massless L
|
||||||
|
sites, those need to be assigned a tiny non-zero mass.
|
||||||
|
|
||||||
|
The table below lists the force field parameters (in real :doc:`units
|
||||||
|
<units>`) to for a the TIP5P model with a cutoff :ref:`(Mahoney)
|
||||||
|
<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
|
||||||
|
long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
|
||||||
|
|
||||||
|
.. list-table::
|
||||||
|
:header-rows: 1
|
||||||
|
:widths: auto
|
||||||
|
|
||||||
|
* - Parameter
|
||||||
|
- TIP5P
|
||||||
|
- TIP5P-E
|
||||||
|
* - O mass (amu)
|
||||||
|
- 15.9994
|
||||||
|
- 15.9994
|
||||||
|
* - H mass (amu)
|
||||||
|
- 1.008
|
||||||
|
- 1.008
|
||||||
|
* - O charge (:math:`e`)
|
||||||
|
- 0.0
|
||||||
|
- 0.0
|
||||||
|
* - L charge (:math:`e`)
|
||||||
|
- -0.241
|
||||||
|
- -0.241
|
||||||
|
* - H charge (:math:`e`)
|
||||||
|
- 0.241
|
||||||
|
- 0.241
|
||||||
|
* - LJ :math:`\epsilon` of OO (kcal/mole)
|
||||||
|
- 0.1600
|
||||||
|
- 0.1780
|
||||||
|
* - LJ :math:`\sigma` of OO (:math:`\AA`)
|
||||||
|
- 3.1200
|
||||||
|
- 3.0970
|
||||||
|
* - LJ :math:`\epsilon` of HH, LL, OH, OL, HL (kcal/mole)
|
||||||
|
- 0.0
|
||||||
|
- 0.0
|
||||||
|
* - LJ :math:`\sigma` of HH, LL, OH, OL, HL (:math:`\AA`)
|
||||||
|
- 1.0
|
||||||
|
- 1.0
|
||||||
|
* - :math:`r_0` of OH bond (:math:`\AA`)
|
||||||
|
- 0.9572
|
||||||
|
- 0.9572
|
||||||
|
* - :math:`\theta_0` of HOH angle
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
- 104.52\ :math:`^{\circ}`
|
||||||
|
* - OL distance (:math:`\AA`)
|
||||||
|
- 0.70
|
||||||
|
- 0.70
|
||||||
|
* - :math:`\theta_0` of LOL angle
|
||||||
|
- 109.47\ :math:`^{\circ}`
|
||||||
|
- 109.47\ :math:`^{\circ}`
|
||||||
|
|
||||||
|
Below is the code for a LAMMPS input file for setting up a simulation of
|
||||||
|
TIP5P water with a molecule file. Because of using :doc:`fix
|
||||||
|
rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
|
||||||
|
extra storage needs to be reserved for them, but we need to switch to
|
||||||
|
atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
|
||||||
|
so that fix rigid/nvt/small can identify rigid bodies by their molecule
|
||||||
|
ID:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
region box block -5 5 -5 5 -5 5
|
||||||
|
create_box 3 box
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
|
mass 2 1.008
|
||||||
|
mass 3 1.0e-100
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/cut 8.0
|
||||||
|
pair_coeff 1 1 0.160 3.12
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
pair_coeff 3 3 0.0 1.0
|
||||||
|
|
||||||
|
fix mol all property/atom mol
|
||||||
|
molecule water tip5p.mol
|
||||||
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
||||||
|
|
||||||
|
timestep 0.20
|
||||||
|
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
|
||||||
|
reset_timestep 0
|
||||||
|
velocity all create 300.0 5463576
|
||||||
|
|
||||||
|
thermo_style custom step temp press etotal density pe ke
|
||||||
|
thermo 1000
|
||||||
|
run 20000
|
||||||
|
write_data tip5p.data nocoeff
|
||||||
|
|
||||||
|
.. _tip5p_molecule:
|
||||||
|
.. code-block::
|
||||||
|
|
||||||
|
# Water molecule. Explicit TIP5P geometry for use with fix rigid
|
||||||
|
|
||||||
|
5 atoms
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 0.00000 -0.06556 0.00000
|
||||||
|
2 0.75695 0.52032 0.00000
|
||||||
|
3 -0.75695 0.52032 0.00000
|
||||||
|
4 0.00000 -0.46971 0.57154
|
||||||
|
5 0.00000 -0.46971 -0.57154
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1 # O
|
||||||
|
2 2 # H
|
||||||
|
3 2 # H
|
||||||
|
4 3 # L
|
||||||
|
5 3 # L
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 0.000
|
||||||
|
2 0.241
|
||||||
|
3 0.241
|
||||||
|
4 -0.241
|
||||||
|
5 -0.241
|
||||||
|
|
||||||
|
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
.. _Mahoney:
|
||||||
|
|
||||||
|
**(Mahoney)** Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
|
||||||
|
|
||||||
|
.. _Rick:
|
||||||
|
|
||||||
|
**(Rick)** Rick, J Chem Phys 120, 6085 (2004)
|
||||||
@ -42,7 +42,7 @@ static linkage, there is no ``liblammps.so`` library file and thus also the
|
|||||||
LAMMPS python module, which depends on it, is not included.
|
LAMMPS python module, which depends on it, is not included.
|
||||||
|
|
||||||
The compressed tar archives available for download have names following
|
The compressed tar archives available for download have names following
|
||||||
the pattern `lammps-linux-x86_64-<version>.tar.gz` and will all unpack
|
the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack
|
||||||
into a ``lammps-static`` folder. The executables are then in the
|
into a ``lammps-static`` folder. The executables are then in the
|
||||||
``lammps-static/bin/`` folder. Since they do not depend on any other
|
``lammps-static/bin/`` folder. Since they do not depend on any other
|
||||||
software, they may be freely moved or copied around.
|
software, they may be freely moved or copied around.
|
||||||
@ -172,7 +172,7 @@ Pre-built EPEL Linux executable
|
|||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
Pre-built LAMMPS (and KIM) packages for stable releases are available
|
Pre-built LAMMPS (and KIM) packages for stable releases are available
|
||||||
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
|
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://docs.fedoraproject.org/en-US/epel/>`_
|
||||||
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
|
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
|
||||||
and compatible Linux distributions. Names of packages, executable,
|
and compatible Linux distributions. Names of packages, executable,
|
||||||
and content are the same as described above for Fedora Linux.
|
and content are the same as described above for Fedora Linux.
|
||||||
|
|||||||
@ -17,11 +17,12 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
|
|||||||
needed to run in parallel with MPI.
|
needed to run in parallel with MPI.
|
||||||
|
|
||||||
The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
|
The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
|
||||||
included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON,
|
included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE,
|
||||||
ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK.
|
ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK. The serial
|
||||||
The serial version also does not include the MPIIO and
|
version also does not include the MPIIO and LATBOLTZ packages. The
|
||||||
LATBOLTZ packages. The GPU package is compiled for OpenCL with
|
PYTHON package is only available in the Python installers that bundle a
|
||||||
mixed precision kernels.
|
Python runtime. The GPU package is compiled for OpenCL with mixed
|
||||||
|
precision kernels.
|
||||||
|
|
||||||
The LAMMPS library is compiled as a shared library and the
|
The LAMMPS library is compiled as a shared library and the
|
||||||
:doc:`LAMMPS Python module <Python_module>` is installed, so that
|
:doc:`LAMMPS Python module <Python_module>` is installed, so that
|
||||||
|
|||||||
@ -195,7 +195,7 @@ Multi-replica models
|
|||||||
* :doc:`parallel replica dynamics <prd>`
|
* :doc:`parallel replica dynamics <prd>`
|
||||||
* :doc:`temperature accelerated dynamics <tad>`
|
* :doc:`temperature accelerated dynamics <tad>`
|
||||||
* :doc:`parallel tempering <temper>`
|
* :doc:`parallel tempering <temper>`
|
||||||
* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
|
* path-integral MD: :doc:`first variant <fix_pimd>`, :doc:`second variant <fix_ipi>`
|
||||||
* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
|
* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
|
||||||
|
|
||||||
.. _prepost:
|
.. _prepost:
|
||||||
|
|||||||
@ -34,5 +34,6 @@ style requirements and recommendations <Modify_style>`.
|
|||||||
Modify_min
|
Modify_min
|
||||||
Modify_region
|
Modify_region
|
||||||
Modify_body
|
Modify_body
|
||||||
|
Modify_gran_sub_mod
|
||||||
Modify_thermo
|
Modify_thermo
|
||||||
Modify_variable
|
Modify_variable
|
||||||
|
|||||||
177
doc/src/Modify_gran_sub_mod.rst
Normal file
177
doc/src/Modify_gran_sub_mod.rst
Normal file
@ -0,0 +1,177 @@
|
|||||||
|
Granular Sub-Model styles
|
||||||
|
===============================
|
||||||
|
|
||||||
|
In granular models, particles are spheres with a finite radius and rotational
|
||||||
|
degrees of freedom as further described in the
|
||||||
|
:doc:`Howto granular page <Howto_granular>`. Interactions between pair of
|
||||||
|
particles or particles and walls may therefore depend on many different modes
|
||||||
|
of motion as described in :doc:`pair granular <pair_granular>` and
|
||||||
|
:doc:`fix wall/gran <fix_wall_gran>`. In both cases, the exchange of forces,
|
||||||
|
torques, and heat flow between two types of bodies is defined using a
|
||||||
|
GranularModel class. The GranularModel class organizes the details of an
|
||||||
|
interaction using a series of granular sub-models each of which describe a
|
||||||
|
particular interaction mode (e.g. normal forces or rolling friction). From a
|
||||||
|
parent GranSubMod class, several types of sub-model classes are derived:
|
||||||
|
|
||||||
|
* GranSubModNormal: normal force sub-model
|
||||||
|
* GranSubModDamping: normal damping sub-model
|
||||||
|
* GranSubModTangential: tangential forces and sliding friction sub-model
|
||||||
|
* GranSubModRolling: rolling friction sub-model
|
||||||
|
* GranSubModTwisting: twisting friction sub-model
|
||||||
|
* GranSubModHeat: heat conduction sub-model
|
||||||
|
|
||||||
|
For each type of sub-model, more classes are further derived, each describing a
|
||||||
|
specific implementation. For instance, from the GranSubModNormal class the
|
||||||
|
GranSubModNormalHooke, GranSubModNormalHertz, and GranSubModNormalJKR classes
|
||||||
|
are derived which calculate Hookean, Hertzian, or JKR normal forces,
|
||||||
|
respectively. This modular structure simplifies the addition of new granular
|
||||||
|
contact models as one only needs to create a new GranSubMod class without
|
||||||
|
having to modify the more complex PairGranular, FixGranWall, and GranularModel
|
||||||
|
classes. Most GranSubMod methods are also already defined by the parent classes
|
||||||
|
so new contact models typically only require edits to a few relevant methods
|
||||||
|
(e.g. methods that define coefficients and calculate forces).
|
||||||
|
|
||||||
|
Each GranSubMod class has a pointer to both the LAMMPS class and the GranularModel
|
||||||
|
class which owns it, ``lmp`` and ``gm``, respectively. The GranularModel class
|
||||||
|
includes several public variables that describe the geometry/dynamics of the
|
||||||
|
contact such as
|
||||||
|
|
||||||
|
.. list-table::
|
||||||
|
|
||||||
|
* - ``xi`` and ``xj``
|
||||||
|
- Positions of the two contacting bodies
|
||||||
|
* - ``vi`` and ``vj``
|
||||||
|
- Velocities of the two contacting bodies
|
||||||
|
* - ``omegai`` and ``omegaj``
|
||||||
|
- Angular velocities of the two contacting bodies
|
||||||
|
* - ``dx`` and ``nx``
|
||||||
|
- The displacement and normalized displacement vectors
|
||||||
|
* - ``r``, ``rsq``, and ``rinv``
|
||||||
|
- The distance, distance squared, and inverse distance
|
||||||
|
* - ``radsum``
|
||||||
|
- The sum of particle radii
|
||||||
|
* - ``vr``, ``vn``, and ``vt``
|
||||||
|
- The relative velocity vector and its normal and tangential components
|
||||||
|
* - ``wr``
|
||||||
|
- The relative rotational velocity
|
||||||
|
|
||||||
|
These quantities, among others, are calculated in the ``GranularModel->check_contact()``
|
||||||
|
and ``GranularModel->calculate_forces()`` methods which can be referred to for more
|
||||||
|
details.
|
||||||
|
|
||||||
|
To create a new GranSubMod class, it is recommended that one first looks at similar
|
||||||
|
GranSubMod classes. All GranSubMod classes share several general methods which may
|
||||||
|
need to be defined
|
||||||
|
|
||||||
|
.. list-table::
|
||||||
|
|
||||||
|
* - ``GranSubMod->mix_coeff()``
|
||||||
|
- Optional method to define how coefficients are mixed for different atom types. By default, coefficients are mixed using a geometric mean.
|
||||||
|
* - ``GranSubMod->coeffs_to_local()``
|
||||||
|
- Parses coefficients to define local variables. Run once at model construction.
|
||||||
|
* - ``GranSubMod->init()``
|
||||||
|
- Optional method to define local variables after other GranSubMod types were created. For instance, this method may be used by a tangential model that derives parameters from the normal model.
|
||||||
|
|
||||||
|
There are also several type-specific methods
|
||||||
|
|
||||||
|
.. list-table::
|
||||||
|
|
||||||
|
* - ``GranSubModNormal->touch()``
|
||||||
|
- Optional method to test when particles are in contact. By default, this is when particles overlap.
|
||||||
|
* - ``GranSubModNormal->pulloff_distance()``
|
||||||
|
- Optional method to return the distance at which particles stop interacting. By default, this is when particles no longer overlap.
|
||||||
|
* - ``GranSubModNormal->calculate_area()``
|
||||||
|
- Optional method to return the surface area of the contact. By default, this returns the geometric cross section.
|
||||||
|
* - ``GranSubModNormal->set_fncrit()``
|
||||||
|
- Optional method that defines the critical force to break the contact used by some tangential, rolling, and twisting sub-models. By default, this is the current total normal force including damping.
|
||||||
|
* - ``GranSubModNormal->calculate_forces()``
|
||||||
|
- Required method that returns the normal contact force
|
||||||
|
* - ``GranSubModDamping->calculate_forces()``
|
||||||
|
- Required method that returns the normal damping force
|
||||||
|
* - ``GranSubModTangential->calculate_forces()``
|
||||||
|
- Required method that calculates tangential forces/torques
|
||||||
|
* - ``GranSubModTwisting->calculate_forces()``
|
||||||
|
- Required method that calculates twisting friction forces/torques
|
||||||
|
* - ``GranSubModRolling->calculate_forces()``
|
||||||
|
- Required method that calculates rolling friction forces/torques
|
||||||
|
* - ``GranSubModHeat->calculate_heat()``
|
||||||
|
- Required method that returns the rate of heat flow
|
||||||
|
|
||||||
|
As an example, say one wanted to create a new normal force option that consisted
|
||||||
|
of a Hookean force with a piecewise stiffness. This could be done by adding a new
|
||||||
|
set of files ``gran_sub_mod_custom.h``:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
#ifdef GranSubMod_CLASS
|
||||||
|
// clang-format off
|
||||||
|
GranSubModStyle(hooke/piecewise,
|
||||||
|
GranSubModNormalHookePiecewise,
|
||||||
|
NORMAL);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef GRAN_SUB_MOD_CUSTOM_H_
|
||||||
|
#define GRAN_SUB_MOD_CUSTOM_H_
|
||||||
|
|
||||||
|
#include "gran_sub_mod.h"
|
||||||
|
#include "gran_sub_mod_normal.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
namespace Granular_NS {
|
||||||
|
|
||||||
|
class GranSubModNormalHookePiecewise : public GranSubModNormal {
|
||||||
|
public:
|
||||||
|
GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
|
||||||
|
void coeffs_to_local() override;
|
||||||
|
double calculate_forces();
|
||||||
|
protected:
|
||||||
|
double k1, k2, delta_switch;
|
||||||
|
};
|
||||||
|
|
||||||
|
} // namespace Granular_NS
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
|
||||||
|
#endif /*GRAN_SUB_MOD_CUSTOM_H_ */
|
||||||
|
#endif /*GRAN_SUB_MOD_CLASS_H_ */
|
||||||
|
|
||||||
|
|
||||||
|
and ``gran_sub_mod_custom.cpp``
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
#include "gran_sub_mod_custom.h"
|
||||||
|
#include "gran_sub_mod_normal.h"
|
||||||
|
#include "granular_model.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace Granular_NS;
|
||||||
|
|
||||||
|
GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
|
||||||
|
{
|
||||||
|
num_coeffs = 4;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void GranSubModNormalHookePiecewise::coeffs_to_local()
|
||||||
|
{
|
||||||
|
k1 = coeffs[0];
|
||||||
|
k2 = coeffs[1];
|
||||||
|
damp = coeffs[2];
|
||||||
|
delta_switch = coeffs[3];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double GranSubModNormalHookePiecewise::calculate_forces()
|
||||||
|
{
|
||||||
|
double Fne;
|
||||||
|
if (gm->delta >= delta_switch) {
|
||||||
|
Fne = k1 * delta_switch + k2 * (gm->delta - delta_switch);
|
||||||
|
} else {
|
||||||
|
Fne = k1 * gm->delta;
|
||||||
|
}
|
||||||
|
return Fne;
|
||||||
|
}
|
||||||
|
|
||||||
@ -2,11 +2,11 @@ Pair styles
|
|||||||
===========
|
===========
|
||||||
|
|
||||||
Classes that compute pairwise non-bonded interactions are derived from
|
Classes that compute pairwise non-bonded interactions are derived from
|
||||||
the Pair class. In LAMMPS, pairwise calculation include many-body
|
the ``Pair`` class. In LAMMPS, pairwise force calculations include
|
||||||
potentials such as EAM, Tersoff, or ReaxFF where particles interact
|
many-body potentials such as EAM, Tersoff, or ReaxFF where particles
|
||||||
without an explicit bond topology but include interactions beyond
|
interact without an explicit bond topology but include interactions
|
||||||
pairwise non-bonded contributions. New styles can be created to add
|
beyond pairwise non-bonded contributions. New styles can be created to
|
||||||
support for additional pair potentials to LAMMPS. When the
|
add support for additional pair potentials to LAMMPS. When the
|
||||||
modifications are small, sometimes it is more effective to derive from
|
modifications are small, sometimes it is more effective to derive from
|
||||||
an existing pair style class. This latter approach is also used by
|
an existing pair style class. This latter approach is also used by
|
||||||
:doc:`Accelerator packages <Speed_packages>` where the accelerated style
|
:doc:`Accelerator packages <Speed_packages>` where the accelerated style
|
||||||
@ -15,10 +15,13 @@ names differ from their base classes by an appended suffix.
|
|||||||
The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
|
The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
|
||||||
very simple potential function. It includes several optional methods to
|
very simple potential function. It includes several optional methods to
|
||||||
enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
|
enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
|
||||||
group/group <compute_group_group>`.
|
group/group <compute_group_group>`. :doc:`Developer_write_pair` contains
|
||||||
|
a detailed discussion of writing new pair styles from scratch, and how
|
||||||
|
simple and more complex pair styles can be implemented with examples
|
||||||
|
from existing pair styles.
|
||||||
|
|
||||||
Here is a brief list of some the class methods in the Pair class that
|
Here is a brief list of some the class methods in the Pair class that
|
||||||
*must* be or *may* be overridden in a derived class.
|
*must* be or *may* be overridden in a derived class for a new pair style.
|
||||||
|
|
||||||
+---------------------------------+---------------------------------------------------------------------+
|
+---------------------------------+---------------------------------------------------------------------+
|
||||||
| Required | "pure" methods that *must* be overridden in a derived class |
|
| Required | "pure" methods that *must* be overridden in a derived class |
|
||||||
|
|||||||
@ -27,140 +27,36 @@ interpreter can find it and installing the LAMMPS shared library into a
|
|||||||
folder that the dynamic loader searches or inside of the installed
|
folder that the dynamic loader searches or inside of the installed
|
||||||
``lammps`` package folder. There are multiple ways to achieve this.
|
``lammps`` package folder. There are multiple ways to achieve this.
|
||||||
|
|
||||||
#. Do a full LAMMPS installation of libraries, executables, selected
|
|
||||||
headers, documentation (if enabled), and supporting files (only
|
|
||||||
available via CMake), which can also be either system-wide or into
|
|
||||||
user specific folders.
|
|
||||||
|
|
||||||
#. Install both components into a Python ``site-packages`` folder, either
|
#. Install both components into a Python ``site-packages`` folder, either
|
||||||
system-wide or in the corresponding user-specific folder. This way no
|
system-wide or in the corresponding user-specific folder. This way no
|
||||||
additional environment variables need to be set, but the shared
|
additional environment variables need to be set, but the shared
|
||||||
library is otherwise not accessible.
|
library is otherwise not accessible.
|
||||||
|
|
||||||
#. Do an installation into a virtual environment. This can either be an
|
#. Do an installation into a virtual environment.
|
||||||
installation of the Python package only or a full installation of LAMMPS.
|
|
||||||
|
|
||||||
#. Leave the files where they are in the source/development tree and
|
#. Leave the files where they are in the source/development tree and
|
||||||
adjust some environment variables.
|
adjust some environment variables.
|
||||||
|
|
||||||
.. tabs::
|
.. tabs::
|
||||||
|
|
||||||
.. tab:: Full install (CMake-only)
|
.. tab:: Python package
|
||||||
|
|
||||||
:ref:`Build the LAMMPS executable and library <library>` with
|
|
||||||
``-DBUILD_SHARED_LIBS=on``, ``-DLAMMPS_EXCEPTIONS=on`` and
|
|
||||||
``-DPKG_PYTHON=on`` (The first option is required, the other two
|
|
||||||
are optional by recommended). The exact file name of the shared
|
|
||||||
library depends on the platform (Unix/Linux, macOS, Windows) and
|
|
||||||
the build configuration being used. The installation base folder
|
|
||||||
is already set by default to the ``$HOME/.local`` directory, but
|
|
||||||
it can be changed to a custom location defined by the
|
|
||||||
``CMAKE_INSTALL_PREFIX`` CMake variable. This uses a folder
|
|
||||||
called ``build`` to store files generated during compilation.
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
# create build folder
|
|
||||||
mkdir build
|
|
||||||
cd build
|
|
||||||
|
|
||||||
# configure LAMMPS compilation
|
|
||||||
cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \
|
|
||||||
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
|
|
||||||
|
|
||||||
# compile LAMMPS
|
|
||||||
cmake --build .
|
|
||||||
|
|
||||||
# install LAMMPS into $HOME/.local
|
|
||||||
cmake --install .
|
|
||||||
|
|
||||||
|
|
||||||
This leads to an installation to the following locations:
|
|
||||||
|
|
||||||
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| File | Location | Notes |
|
|
||||||
+========================+=================================================================+=============================================================+
|
|
||||||
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
|
|
||||||
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
|
|
||||||
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS shared library | * ``$HOME/.local/lib/`` (32bit) | Set shared loader environment variable to this path |
|
|
||||||
| | * ``$HOME/.local/lib64/`` (64bit) | (see below for more info on this) |
|
|
||||||
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS executable | * ``$HOME/.local/bin/`` | |
|
|
||||||
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
|
|
||||||
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
|
|
||||||
For a system-wide installation you need to set
|
|
||||||
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
|
|
||||||
``/usr/local``); the default is ``${HOME}/.local``. The
|
|
||||||
installation step for a system folder installation (**not** the
|
|
||||||
configuration/compilation) needs to be done with superuser
|
|
||||||
privilege, e.g. by using ``sudo cmake --install .``. The
|
|
||||||
installation folders will then be changed to (assuming ``/usr`` as
|
|
||||||
prefix):
|
|
||||||
|
|
||||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| File | Location | Notes |
|
|
||||||
+========================+=========================================================+=============================================================+
|
|
||||||
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
|
|
||||||
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
|
|
||||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS shared library | * ``/usr/lib/`` (32bit) | |
|
|
||||||
| | * ``/usr/lib64/`` (64bit) | |
|
|
||||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS executable | * ``/usr/bin/`` | |
|
|
||||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS potential files | * ``/usr/share/lammps/potentials/`` | |
|
|
||||||
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
|
|
||||||
To be able to use the "user" installation you have to ensure that
|
|
||||||
the folder containing the LAMMPS shared library is either included
|
|
||||||
in a path searched by the shared linker (e.g. like
|
|
||||||
``/usr/lib64/``) or part of the ``LD_LIBRARY_PATH`` environment
|
|
||||||
variable (or ``DYLD_LIBRARY_PATH`` on macOS). Otherwise you will
|
|
||||||
get an error when trying to create a LAMMPS object through the
|
|
||||||
Python module.
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
# Unix/Linux
|
|
||||||
export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
|
|
||||||
|
|
||||||
# macOS
|
|
||||||
export DYLD_LIBRARY_PATH=$HOME/.local/lib:$DYLD_LIBRARY_PATH
|
|
||||||
|
|
||||||
If you plan to use the LAMMPS executable (e.g., ``lmp``), you may
|
|
||||||
also need to adjust the ``PATH`` environment variable (but many
|
|
||||||
newer Linux distributions already have ``$HOME/.local/bin``
|
|
||||||
included). Example:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
export PATH=$HOME/.local/bin:$PATH
|
|
||||||
|
|
||||||
To make those changes permanent, you can add the commands to your
|
|
||||||
``$HOME/.bashrc`` file. For a system-wide installation is is not
|
|
||||||
necessary due to files installed in system folders that are loaded
|
|
||||||
automatically when a login shell is started.
|
|
||||||
|
|
||||||
.. tab:: Python package only
|
|
||||||
|
|
||||||
Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
|
Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
|
||||||
:doc:`traditional make <Build_make>` procedure in :ref:`shared
|
:doc:`traditional make <Build_make>` procedure in :ref:`shared
|
||||||
mode <exe>`. After compilation has finished type (in the
|
mode <exe>`. After compilation has finished, type (in the
|
||||||
compilation folder):
|
compilation folder):
|
||||||
|
|
||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
make install-python
|
make install-python
|
||||||
|
|
||||||
This will try to build a so-called (binary) 'wheel', a compressed
|
This will try to build a so-called (binary) wheel file, a
|
||||||
binary python package and then install it with the python package
|
compressed binary python package and then install it with the
|
||||||
manager 'pip'. Installation will be attempted into a system-wide
|
python package manager 'pip'. Installation will be attempted into
|
||||||
``site-packages`` folder and if that fails into the corresponding
|
a system-wide ``site-packages`` folder and if that fails into the
|
||||||
folder in the user's home directory. For a system-wide installation you
|
corresponding folder in the user's home directory. For a
|
||||||
would have to gain superuser privilege, e.g. though ``sudo``
|
system-wide installation you usually would have to gain superuser
|
||||||
|
privilege first, e.g. though ``sudo``
|
||||||
|
|
||||||
+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
|
+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
|
||||||
| File | Location | Notes |
|
| File | Location | Notes |
|
||||||
@ -211,10 +107,11 @@ folder that the dynamic loader searches or inside of the installed
|
|||||||
|
|
||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
python install.py -p <python package> -l <shared library> [-n]
|
python install.py -p <python package> -l <shared library> -v <version.h file> [-n]
|
||||||
|
|
||||||
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
|
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
|
||||||
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
|
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
|
||||||
|
* the ``-v`` flag points to the LAMMPS version header file to extract the version date,
|
||||||
* and the optional ``-n`` instructs the script to only build a wheel file
|
* and the optional ``-n`` instructs the script to only build a wheel file
|
||||||
but not attempt to install it.
|
but not attempt to install it.
|
||||||
|
|
||||||
@ -272,38 +169,6 @@ folder that the dynamic loader searches or inside of the installed
|
|||||||
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
|
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
||||||
|
|
||||||
If you do a full installation (CMake only) with "install", this
|
|
||||||
leads to the following installation locations:
|
|
||||||
|
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| File | Location | Notes |
|
|
||||||
+========================+========================================================+=============================================================+
|
|
||||||
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
|
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
|
|
||||||
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
|
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
|
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
|
|
||||||
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
|
|
||||||
|
|
||||||
In that case you need to modify the ``$HOME/myenv/bin/activate``
|
|
||||||
script in a similar fashion you need to update your
|
|
||||||
``$HOME/.bashrc`` file to include the shared library and
|
|
||||||
executable locations in ``LD_LIBRARY_PATH`` (or
|
|
||||||
``DYLD_LIBRARY_PATH`` on macOS) and ``PATH``, respectively.
|
|
||||||
|
|
||||||
For example with:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
# Unix/Linux
|
|
||||||
echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
|
|
||||||
|
|
||||||
# macOS
|
|
||||||
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
|
|
||||||
|
|
||||||
.. tab:: In place usage
|
.. tab:: In place usage
|
||||||
|
|
||||||
You can also :doc:`compile LAMMPS <Build>` as usual in
|
You can also :doc:`compile LAMMPS <Build>` as usual in
|
||||||
|
|||||||
@ -320,7 +320,8 @@ eam generate tool
|
|||||||
-----------------------------
|
-----------------------------
|
||||||
|
|
||||||
The tools/eam_generate directory contains several one-file C programs
|
The tools/eam_generate directory contains several one-file C programs
|
||||||
that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) <pair_eam>` setfl potential file. The potentials they
|
that convert an analytic formula into a tabulated :doc:`embedded atom
|
||||||
|
method (EAM) <pair_eam>` setfl potential file. The potentials they
|
||||||
produce are in the potentials directory, and can be used with the
|
produce are in the potentials directory, and can be used with the
|
||||||
:doc:`pair_style eam/alloy <pair_eam>` command.
|
:doc:`pair_style eam/alloy <pair_eam>` command.
|
||||||
|
|
||||||
|
|||||||
@ -161,15 +161,14 @@ and each stores a per-particle diameter and mass. If the diameter >
|
|||||||
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
|
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
|
||||||
is a point particle. Note that by use of the *disc* keyword with the
|
is a point particle. Note that by use of the *disc* keyword with the
|
||||||
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
|
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
|
||||||
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
|
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
|
||||||
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
|
:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
|
||||||
can be effectively treated as 2d discs for a 2d simulation if desired.
|
spheres can be effectively treated as 2d discs for a 2d simulation if
|
||||||
See also the :doc:`set density/disc <set>` command. The *sphere* and
|
desired. See also the :doc:`set density/disc <set>` command. These
|
||||||
*bpm/sphere* styles take an optional 0 or 1 argument. A value of 0
|
styles take an optional 0 or 1 argument. A value of 0 means the
|
||||||
means the radius of each sphere is constant for the duration of the
|
radius of each sphere is constant for the duration of the simulation.
|
||||||
simulation. A value of 1 means the radii may vary dynamically during
|
A value of 1 means the radii may vary dynamically during the simulation,
|
||||||
the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
|
e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
|
||||||
command.
|
|
||||||
|
|
||||||
For the *ellipsoid* style, the particles are ellipsoids and each
|
For the *ellipsoid* style, the particles are ellipsoids and each
|
||||||
stores a flag which indicates whether it is a finite-size ellipsoid or
|
stores a flag which indicates whether it is a finite-size ellipsoid or
|
||||||
|
|||||||
@ -53,6 +53,7 @@ Syntax
|
|||||||
name = name of the atom-style variable
|
name = name of the atom-style variable
|
||||||
*store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
|
*store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
|
||||||
name = atom property name (without d\_ prefix)
|
name = atom property name (without d\_ prefix)
|
||||||
|
*sort* arg = *no* or *yes*
|
||||||
*out* arg = filename
|
*out* arg = filename
|
||||||
filename = write each processor's subdomain to a file
|
filename = write each processor's subdomain to a file
|
||||||
|
|
||||||
@ -492,6 +493,14 @@ different kinds of custom atom vectors or arrays as arguments.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
The *sort* keyword determines whether the communication of per-atom
|
||||||
|
data to other processors during load-balancing will be random or
|
||||||
|
deterministic. Random is generally faster; deterministic will ensure
|
||||||
|
the new ordering of atoms on each processor is the same each time the
|
||||||
|
same simulation is run. This can be useful for debugging purposes.
|
||||||
|
Since the balance command is a one-time operation, the default is
|
||||||
|
*yes* to perform sorting.
|
||||||
|
|
||||||
The *out* keyword writes a text file to the specified *filename* with
|
The *out* keyword writes a text file to the specified *filename* with
|
||||||
the results of the balancing operation. The file contains the bounds
|
the results of the balancing operation. The file contains the bounds
|
||||||
of the subdomain for each processor after the balancing operation
|
of the subdomain for each processor after the balancing operation
|
||||||
@ -569,4 +578,5 @@ Related commands
|
|||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
none
|
The default setting is sort = yes.
|
||||||
|
|
||||||
|
|||||||
@ -10,7 +10,7 @@ Syntax
|
|||||||
|
|
||||||
bond_style bpm/rotational keyword value attribute1 attribute2 ...
|
bond_style bpm/rotational keyword value attribute1 attribute2 ...
|
||||||
|
|
||||||
* optional keyword = *overlay/pair* or *store/local* or *smooth*
|
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -30,6 +30,9 @@ Syntax
|
|||||||
*smooth* value = *yes* or *no*
|
*smooth* value = *yes* or *no*
|
||||||
smooths bond forces near the breaking point
|
smooths bond forces near the breaking point
|
||||||
|
|
||||||
|
*break/no*
|
||||||
|
indicates that bonds should not break during a run
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
@ -140,6 +143,12 @@ the *overlay/pair* keyword. These settings require specific
|
|||||||
restrictions. Further details can be found in the `:doc: how to
|
restrictions. Further details can be found in the `:doc: how to
|
||||||
<Howto_BPM>` page on BPMs.
|
<Howto_BPM>` page on BPMs.
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
|
||||||
|
during a simulation run. This will prevent some unnecessary calculation.
|
||||||
|
However, if a bond does break, it will trigger an error.
|
||||||
|
|
||||||
If the *store/local* keyword is used, an internal fix will track bonds that
|
If the *store/local* keyword is used, an internal fix will track bonds that
|
||||||
break during the simulation. Whenever a bond breaks, data is processed
|
break during the simulation. Whenever a bond breaks, data is processed
|
||||||
and transferred to an internal fix labeled *fix_ID*. This allows the
|
and transferred to an internal fix labeled *fix_ID*. This allows the
|
||||||
|
|||||||
@ -10,7 +10,7 @@ Syntax
|
|||||||
|
|
||||||
bond_style bpm/spring keyword value attribute1 attribute2 ...
|
bond_style bpm/spring keyword value attribute1 attribute2 ...
|
||||||
|
|
||||||
* optional keyword = *overlay/pair* or *store/local* or *smooth*
|
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -30,6 +30,9 @@ Syntax
|
|||||||
*smooth* value = *yes* or *no*
|
*smooth* value = *yes* or *no*
|
||||||
smooths bond forces near the breaking point
|
smooths bond forces near the breaking point
|
||||||
|
|
||||||
|
*break/no*
|
||||||
|
indicates that bonds should not break during a run
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
@ -47,7 +50,7 @@ Description
|
|||||||
|
|
||||||
.. versionadded:: 4May2022
|
.. versionadded:: 4May2022
|
||||||
|
|
||||||
The *bpm/spring* bond style computes forces and torques based on
|
The *bpm/spring* bond style computes forces based on
|
||||||
deviations from the initial reference state of the two atoms. The
|
deviations from the initial reference state of the two atoms. The
|
||||||
reference state is stored by each bond when it is first computed in
|
reference state is stored by each bond when it is first computed in
|
||||||
the setup of a run. Data is then preserved across run commands and is
|
the setup of a run. Data is then preserved across run commands and is
|
||||||
@ -56,7 +59,8 @@ the system will not reset the reference state of a bond.
|
|||||||
|
|
||||||
This bond style only applies central-body forces which conserve the
|
This bond style only applies central-body forces which conserve the
|
||||||
translational and rotational degrees of freedom of a bonded set of
|
translational and rotational degrees of freedom of a bonded set of
|
||||||
particles. The force has a magnitude of
|
particles based on a model described by Clemmer and Robbins
|
||||||
|
:ref:`(Clemmer) <fragment-Clemmer>`. The force has a magnitude of
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -105,6 +109,12 @@ the *overlay/pair* keyword. These settings require specific
|
|||||||
restrictions. Further details can be found in the `:doc: how to
|
restrictions. Further details can be found in the `:doc: how to
|
||||||
<Howto_BPM>` page on BPMs.
|
<Howto_BPM>` page on BPMs.
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
|
||||||
|
during a simulation run. This will prevent some unnecessary calculation.
|
||||||
|
However, if a bond does break, it will trigger an error.
|
||||||
|
|
||||||
If the *store/local* keyword is used, an internal fix will track bonds that
|
If the *store/local* keyword is used, an internal fix will track bonds that
|
||||||
break during the simulation. Whenever a bond breaks, data is processed
|
break during the simulation. Whenever a bond breaks, data is processed
|
||||||
and transferred to an internal fix labeled *fix_ID*. This allows the
|
and transferred to an internal fix labeled *fix_ID*. This allows the
|
||||||
@ -200,6 +210,10 @@ The option defaults are *smooth* = *yes*
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
.. _fragment-Clemmer:
|
||||||
|
|
||||||
|
**(Clemmer)** Clemmer and Robbins, Phys. Rev. Lett. (2022).
|
||||||
|
|
||||||
.. _Groot4:
|
.. _Groot4:
|
||||||
|
|
||||||
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
||||||
|
|||||||
@ -51,7 +51,7 @@ in the same form as in pair style :doc:`nm/cut <pair_nm>`. The bond energy is th
|
|||||||
|
|
||||||
.. math::
|
.. 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]
|
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
|
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
|
the potential minimum, :math:`r_0`, to be repulsive only. The following
|
||||||
|
|||||||
90
doc/src/bond_harmonic_restrain.rst
Normal file
90
doc/src/bond_harmonic_restrain.rst
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
.. index:: bond_style harmonic/restrain
|
||||||
|
|
||||||
|
bond_style harmonic/restrain command
|
||||||
|
====================================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
bond_style harmonic/restrain
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 5 80.0
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
The *harmonic/restrain* bond style uses the potential
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
E = K (r - r_{t=0})^2
|
||||||
|
|
||||||
|
where :math:`r_{t=0}` is the distance between the bonded atoms at the
|
||||||
|
beginning of the first :doc:`run <run>` or :doc:`minimize <minimize>`
|
||||||
|
command after the bond style has been defined (*t=0*). Note that the
|
||||||
|
usual 1/2 factor is included in :math:`K`. This will effectively
|
||||||
|
restrain bonds to their initial length, whatever that is. This is where
|
||||||
|
this bond style differs from :doc:`bond style harmonic <bond_harmonic>`
|
||||||
|
where the bond length is set through the per bond type coefficients.
|
||||||
|
|
||||||
|
The following coefficient 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)
|
||||||
|
|
||||||
|
This bond style differs from other options to add harmonic restraints
|
||||||
|
like :doc:`fix restrain <fix_restrain>` or :doc:`pair style list
|
||||||
|
<pair_list>` or :doc:`fix colvars <fix_colvars>` in that it requires a
|
||||||
|
bond topology, and thus the defined bonds will trigger exclusion of
|
||||||
|
special neighbors from the neighbor list according to the
|
||||||
|
:doc:`special_bonds <special_bonds>` settings.
|
||||||
|
|
||||||
|
Restart info
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This bond style supports the :doc:`write_restart <write_restart>` and
|
||||||
|
:doc:`read_restart <read_restart>` commands. The state of the initial
|
||||||
|
bond lengths is stored with restart files and read back.
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This 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.
|
||||||
|
|
||||||
|
This bond style maintains internal data to determine the original bond
|
||||||
|
lengths :math:`r_{t=0}`. This information will be written to
|
||||||
|
:doc:`binary restart files <write_restart>` but **not** to :doc:`data
|
||||||
|
files <write_data>`. Thus, continuing a simulation is *only* possible
|
||||||
|
with :doc:`read_restart <read_restart>`. When using the :doc:`read_data
|
||||||
|
command <read_data>`, the reference bond lengths :math:`r_{t=0}` will be
|
||||||
|
re-initialized from the current geometry.
|
||||||
|
|
||||||
|
This bond style cannot be used with :doc:`fix shake or fix rattle
|
||||||
|
<fix_shake>`, with :doc:`fix filter/corotate <fix_filter_corotate>`, or
|
||||||
|
any :doc:`tip4p pair style <pair_lj_cut_tip4p>` since there is no specific
|
||||||
|
equilibrium distance for a given bond type.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`bond_coeff <bond_coeff>`, :doc:`bond_harmonic <bond_harmonic>`,
|
||||||
|
:doc:`fix restrain <fix_restrain>`, :doc:`pair style list <pair_list>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
@ -10,7 +10,7 @@ Syntax
|
|||||||
|
|
||||||
bond_style style args
|
bond_style style args
|
||||||
|
|
||||||
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
|
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
|
||||||
|
|
||||||
* args = none for any style except *hybrid*
|
* args = none for any style except *hybrid*
|
||||||
|
|
||||||
@ -93,6 +93,7 @@ accelerated styles exist.
|
|||||||
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
|
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
|
||||||
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
|
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
|
||||||
* :doc:`harmonic <bond_harmonic>` - harmonic bond
|
* :doc:`harmonic <bond_harmonic>` - harmonic bond
|
||||||
|
* :doc:`harmonic/restrain <bond_harmonic_restrain>` - harmonic bond to restrain to original bond distance
|
||||||
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
|
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
|
||||||
* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
|
* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
|
||||||
* :doc:`lepton <bond_lepton>` - bond potential from evaluating a string
|
* :doc:`lepton <bond_lepton>` - bond potential from evaluating a string
|
||||||
|
|||||||
@ -112,8 +112,9 @@ are estimated (less accurately) by the first two and last two force
|
|||||||
values in the table.
|
values in the table.
|
||||||
|
|
||||||
The "EQ" parameter is also optional. If used, it is followed by a the
|
The "EQ" parameter is also optional. If used, it is followed by a the
|
||||||
equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix_shake>` command. If not used, the equilibrium bond
|
equilibrium bond length, which is used, for example, by the :doc:`fix
|
||||||
length is to the distance in the table with the lowest potential energy.
|
shake <fix_shake>` command. If not used, the equilibrium bond length is
|
||||||
|
to the distance in the table with the lowest potential energy.
|
||||||
|
|
||||||
Following a blank line, the next N lines list the tabulated values.
|
Following a blank line, the next N lines list the tabulated values.
|
||||||
On each line, the first value is the index from 1 to N, the second value is
|
On each line, the first value is the index from 1 to N, the second value is
|
||||||
@ -135,16 +136,15 @@ one that matches the specified keyword.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This bond style writes the settings for the "bond_style table"
|
This bond style writes the settings for the "bond_style table" command
|
||||||
command to :doc:`binary restart files <restart>`, so a bond_style
|
to :doc:`binary restart files <restart>`, so a bond_style command does
|
||||||
command does not need to specified in an input script that reads a
|
not need to specified in an input script that reads a restart file.
|
||||||
restart file. However, the coefficient information is not stored in
|
However, the coefficient information is not stored in the restart file,
|
||||||
the restart file, since it is tabulated in the potential files. Thus,
|
since it is tabulated in the potential files. Thus, bond_coeff commands
|
||||||
bond_coeff commands do need to be specified in the restart input
|
do need to be specified in the restart input script.
|
||||||
script.
|
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|||||||
@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`bond_style table <bond_table>`, `angle_write <angle_write>`,
|
:doc:`bond_style table <bond_table>`, :doc:`angle_write <angle_write>`,
|
||||||
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
|
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
|
|||||||
@ -69,6 +69,7 @@ For many systems this is an efficient algorithm, but for systems with
|
|||||||
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
|
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
|
||||||
be faster. In *multi*, each atom is assigned to a collection which should
|
be faster. In *multi*, each atom is assigned to a collection which should
|
||||||
correspond to a set of atoms with similar interaction cutoffs.
|
correspond to a set of atoms with similar interaction cutoffs.
|
||||||
|
See the :doc:`neighbor <neighbor>` command for a detailed description of collections.
|
||||||
In this case, each atom collection is assigned its own distance
|
In this case, each atom collection is assigned its own distance
|
||||||
cutoff for communication purposes, and fewer atoms will be
|
cutoff for communication purposes, and fewer atoms will be
|
||||||
communicated. in *multi/old*, a similar technique is used but atoms
|
communicated. in *multi/old*, a similar technique is used but atoms
|
||||||
|
|||||||
@ -206,6 +206,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
|||||||
* :doc:`dilatation/atom <compute_dilatation_atom>` - Peridynamic dilatation for each atom
|
* :doc:`dilatation/atom <compute_dilatation_atom>` - Peridynamic dilatation for each atom
|
||||||
* :doc:`dipole <compute_dipole>` - dipole vector and total dipole
|
* :doc:`dipole <compute_dipole>` - dipole vector and total dipole
|
||||||
* :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
|
* :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
|
||||||
|
* :doc:`dipole/tip4p <compute_dipole>` - dipole vector and total dipole with TIP4P pair style
|
||||||
|
* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk with TIP4P pair style
|
||||||
* :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
|
* :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
|
||||||
* :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
|
* :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
|
||||||
* :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature
|
* :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature
|
||||||
@ -258,6 +260,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
|||||||
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
|
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
|
||||||
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
|
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
|
||||||
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
|
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
|
||||||
|
* :doc:`pressure/alchemy <compute_pressure_alchemy>` - mixed system total pressure and pressure tensor for :doc:`fix alchemy <fix_alchemy>` runs
|
||||||
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
|
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
|
||||||
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
|
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
|
||||||
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
|
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
|
||||||
|
|||||||
@ -1,6 +1,10 @@
|
|||||||
.. index:: compute dipole
|
.. index:: compute dipole
|
||||||
|
.. index:: compute dipole/tip4p
|
||||||
|
|
||||||
compute dipole command
|
compute dipole command
|
||||||
|
======================
|
||||||
|
|
||||||
|
compute dipole/tip4p command
|
||||||
============================
|
============================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
@ -8,10 +12,10 @@ Syntax
|
|||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
compute ID group-ID dipole arg
|
compute ID group-ID style arg
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||||
* dipole = style name of this compute command
|
* style = *dipole* or *dipole/tip4p*
|
||||||
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
|
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
@ -21,6 +25,7 @@ Examples
|
|||||||
|
|
||||||
compute 1 fluid dipole
|
compute 1 fluid dipole
|
||||||
compute dw water dipole geometry
|
compute dw water dipole geometry
|
||||||
|
compute dw water dipole/tip4p
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -28,13 +33,20 @@ Description
|
|||||||
Define a computation that calculates the dipole vector and total dipole
|
Define a computation that calculates the dipole vector and total dipole
|
||||||
for a group of atoms.
|
for a group of atoms.
|
||||||
|
|
||||||
This compute calculates the x,y,z coordinates of the dipole vector
|
These computes calculate the x,y,z coordinates of the dipole vector and
|
||||||
and the total dipole moment for the atoms in the compute group.
|
the total dipole moment for the atoms in the compute group. This
|
||||||
This includes all effects due to atoms passing through periodic boundaries.
|
includes all effects due to atoms passing through periodic boundaries.
|
||||||
For a group with a net charge the resulting dipole is made position independent
|
For a group with a net charge the resulting dipole is made position
|
||||||
by subtracting the position vector of the center of mass or geometric center
|
independent by subtracting the position vector of the center of mass or
|
||||||
times the net charge from the computed dipole vector. Both per-atom charges
|
geometric center times the net charge from the computed dipole
|
||||||
and per-atom dipole moments, if present, contribute to the computed dipole.
|
vector. Both per-atom charges and per-atom dipole moments, if present,
|
||||||
|
contribute to the computed dipole.
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
Compute *dipole/tip4p* includes adjustments for the charge carrying
|
||||||
|
point M in molecules with TIP4P water geometry. The corresponding
|
||||||
|
parameters are extracted from the pair style.
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
@ -49,10 +61,10 @@ and per-atom dipole moments, if present, contribute to the computed dipole.
|
|||||||
Output info
|
Output info
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This compute calculations a global scalar containing the magnitude of
|
These computes calculate a global scalar containing the magnitude of the
|
||||||
the computed dipole moment and a global vector of length 3 with the
|
computed dipole moment and a global vector of length 3 with the dipole
|
||||||
dipole vector. See the :doc:`Howto output <Howto_output>` page for
|
vector. See the :doc:`Howto output <Howto_output>` page for an overview
|
||||||
an overview of LAMMPS output options.
|
of LAMMPS output options.
|
||||||
|
|
||||||
The computed values are "intensive". The array values will be in
|
The computed values are "intensive". The array values will be in
|
||||||
dipole units (i.e., charge :doc:`units <units>` times distance
|
dipole units (i.e., charge :doc:`units <units>` times distance
|
||||||
@ -60,7 +72,12 @@ dipole units (i.e., charge :doc:`units <units>` times distance
|
|||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
none
|
|
||||||
|
Compute style *dipole/tip4p* 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.
|
||||||
|
|
||||||
|
Compute style *dipole/tip4p* can only be used with tip4p pair styles.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -1,17 +1,21 @@
|
|||||||
.. index:: compute dipole/chunk
|
.. index:: compute dipole/chunk
|
||||||
|
.. index:: compute dipole/tip4p/chunk
|
||||||
|
|
||||||
compute dipole/chunk command
|
compute dipole/chunk command
|
||||||
============================
|
============================
|
||||||
|
|
||||||
|
compute dipole/tip4p/chunk command
|
||||||
|
==================================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
compute ID group-ID dipole/chunk chunkID arg
|
compute ID group-ID style chunkID arg
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||||
* dipole/chunk = style name of this compute command
|
* style = *dipole/chunk* or *dipole/tip4p/chunk*
|
||||||
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
|
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
|
||||||
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
|
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
|
||||||
|
|
||||||
@ -38,13 +42,20 @@ or atoms in a spatial bin. See the :doc:`compute chunk/atom
|
|||||||
details of how chunks can be defined and examples of how they can be
|
details of how chunks can be defined and examples of how they can be
|
||||||
used to measure properties of a system.
|
used to measure properties of a system.
|
||||||
|
|
||||||
This compute calculates the :math:`(x,y,z)` coordinates of the dipole vector
|
These computes calculate the :math:`(x,y,z)` coordinates of the dipole
|
||||||
and the total dipole moment for each chunk, which includes all effects due
|
vector and the total dipole moment for each chunk, which includes all
|
||||||
to atoms passing through periodic boundaries. For chunks with a net
|
effects due to atoms passing through periodic boundaries. For chunks
|
||||||
charge the resulting dipole is made position independent by subtracting
|
with a net charge the resulting dipole is made position independent by
|
||||||
the position vector of the center of mass or geometric center times the
|
subtracting the position vector of the center of mass or geometric
|
||||||
net charge from the computed dipole vector. Both per-atom charges and
|
center times the net charge from the computed dipole vector. Both
|
||||||
per-atom dipole moments, if present, contribute to the computed dipole.
|
per-atom charges and per-atom dipole moments, if present, contribute to
|
||||||
|
the computed dipole.
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
Compute *dipole/tip4p/chunk* includes adjustments for the charge
|
||||||
|
carrying point M in molecules with TIP4P water geometry. The
|
||||||
|
corresponding parameters are extracted from the pair style.
|
||||||
|
|
||||||
Note that only atoms in the specified group contribute to the
|
Note that only atoms in the specified group contribute to the
|
||||||
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
|
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
|
||||||
@ -78,12 +89,12 @@ command, for example:
|
|||||||
Output info
|
Output info
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This compute calculates a global array where the number of rows = the
|
These computes calculate a global array where the number of rows = the
|
||||||
number of chunks *Nchunk* as calculated by the specified :doc:`compute
|
number of chunks *Nchunk* as calculated by the specified :doc:`compute
|
||||||
chunk/atom <compute_chunk_atom>` command. The number of columns is 4 for
|
chunk/atom <compute_chunk_atom>` command. The number of columns is 4
|
||||||
the :math:`(x,y,z)` dipole vector components and the total dipole of each
|
for the :math:`(x,y,z)` dipole vector components and the total dipole of
|
||||||
chunk. These values can be accessed by any command that uses global
|
each chunk. These values can be accessed by any command that uses
|
||||||
array values from a compute as input. See the :doc:`Howto output
|
global array values from a compute as input. See the :doc:`Howto output
|
||||||
<Howto_output>` page for an overview of LAMMPS output options.
|
<Howto_output>` page for an overview of LAMMPS output options.
|
||||||
|
|
||||||
The array values are "intensive". The array values will be in
|
The array values are "intensive". The array values will be in
|
||||||
@ -92,7 +103,13 @@ dipole units (i.e., charge :doc:`units <units>` times distance
|
|||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
none
|
|
||||||
|
Compute style *dipole/tip4p/chunk* 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.
|
||||||
|
|
||||||
|
Compute style *dipole/tip4p/chunk* can only be used with tip4p pair
|
||||||
|
styles.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
80
doc/src/compute_pressure_alchemy.rst
Normal file
80
doc/src/compute_pressure_alchemy.rst
Normal file
@ -0,0 +1,80 @@
|
|||||||
|
.. index:: compute pressure/alchemy
|
||||||
|
|
||||||
|
compute pressure/alchemy command
|
||||||
|
================================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
compute ID group-ID pressure/alchemy fix-ID
|
||||||
|
|
||||||
|
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||||
|
* pressure/alchemy = style name of this compute command
|
||||||
|
* fix-ID = ID of :doc:`fix alchemy <fix_alchemy>` command
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix trans all alchemy
|
||||||
|
compute mixed all pressure/alchemy trans
|
||||||
|
thermo_modify press mixed
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
Define a compute style that makes the "mixed" system pressure available
|
||||||
|
for a system that uses the :doc:`fix alchemy <fix_alchemy>` command to
|
||||||
|
transform one topology to another. This can be used in combination with
|
||||||
|
either :doc:`thermo_modify press <thermo_modify>` or :doc:`fix_modify
|
||||||
|
press <fix_modify>` to output and access a pressure consistent with the
|
||||||
|
simulated combined two topology system.
|
||||||
|
|
||||||
|
The actual pressure is determined with :doc:`compute pressure
|
||||||
|
<compute_pressure>` commands that are internally used by :doc:`fix
|
||||||
|
alchemy <fix_alchemy>` for each topology individually and then combined.
|
||||||
|
This command just extracts the information from the fix.
|
||||||
|
|
||||||
|
The ``examples/PACKAGES/alchemy`` folder contains an example input for this command.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Output info
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
This compute calculates a global scalar (the pressure) and a global
|
||||||
|
vector of length 6 (the pressure tensor), which can be accessed by
|
||||||
|
indices 1--6. These values can be used by any command that uses global
|
||||||
|
scalar or vector values from a compute as input. See the :doc:`Howto
|
||||||
|
output <Howto_output>` page for an overview of LAMMPS output options.
|
||||||
|
|
||||||
|
The ordering of values in the symmetric pressure tensor is as follows:
|
||||||
|
:math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},`
|
||||||
|
:math:`p_{xz},` :math:`p_{yz}.`
|
||||||
|
|
||||||
|
The scalar and vector values calculated by this compute are "intensive".
|
||||||
|
The scalar and vector values will be in pressure :doc:`units <units>`.
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This compute is part of the REPLICA 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:`fix alchemy <fix_alchemy>`, :doc:`compute pressure <compute_pressure>`,
|
||||||
|
:doc:`thermo_modify <thermo_modify>`, :doc:`fix_modify <fix_modify>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
@ -111,6 +111,7 @@ Syntax
|
|||||||
q, mux, muy, muz, mu,
|
q, mux, muy, muz, mu,
|
||||||
radius, diameter, omegax, omegay, omegaz,
|
radius, diameter, omegax, omegay, omegaz,
|
||||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||||
|
heatflow, temperature,
|
||||||
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
|
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
|
||||||
i_name, d_name, i2_name[I], d2_name[I]
|
i_name, d_name, i2_name[I], d2_name[I]
|
||||||
|
|
||||||
@ -137,6 +138,8 @@ Syntax
|
|||||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||||
tqx,tqy,tqz = torque on finite-size particles
|
tqx,tqy,tqz = torque on finite-size particles
|
||||||
|
heatflow = rate of heat flow into particle
|
||||||
|
temperature = temperature of particle
|
||||||
c_ID = per-atom vector calculated by a compute with ID
|
c_ID = per-atom vector calculated by a compute with ID
|
||||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
||||||
f_ID = per-atom vector calculated by a fix with ID
|
f_ID = per-atom vector calculated by a fix with ID
|
||||||
@ -375,7 +378,7 @@ output with each snapshot:
|
|||||||
nx ny nz
|
nx ny nz
|
||||||
|
|
||||||
The value dim will be 2 or 3 for 2d or 3d simulations. It is included
|
The value dim will be 2 or 3 for 2d or 3d simulations. It is included
|
||||||
so that post-processing tools like `OVITO <https://www.ovito.org>`,
|
so that post-processing tools like `OVITO <https://www.ovito.org>`_,
|
||||||
which can visualize grid-based quantities know how to draw each grid
|
which can visualize grid-based quantities know how to draw each grid
|
||||||
cell. The grid size will match the input script parameters for
|
cell. The grid size will match the input script parameters for
|
||||||
grid(s) created by the computes or fixes which are referenced by the
|
grid(s) created by the computes or fixes which are referenced by the
|
||||||
|
|||||||
@ -181,6 +181,7 @@ accelerated styles exist.
|
|||||||
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
|
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
|
||||||
* :doc:`addforce <fix_addforce>` - add a force to each atom
|
* :doc:`addforce <fix_addforce>` - add a force to each atom
|
||||||
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
|
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
|
||||||
|
* :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
|
||||||
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
|
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
|
||||||
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>` - 6-body terms in AMOEBA force field
|
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>` - 6-body terms in AMOEBA force field
|
||||||
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
|
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
|
||||||
@ -221,6 +222,7 @@ accelerated styles exist.
|
|||||||
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
|
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
|
||||||
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
|
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
|
||||||
* :doc:`efield <fix_efield>` - impose electric field on system
|
* :doc:`efield <fix_efield>` - impose electric field on system
|
||||||
|
* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
|
||||||
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
|
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
|
||||||
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
|
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
|
||||||
* :doc:`electrode/conq <fix_electrode>` - impose total electric charge
|
* :doc:`electrode/conq <fix_electrode>` - impose total electric charge
|
||||||
@ -244,6 +246,7 @@ accelerated styles exist.
|
|||||||
* :doc:`grem <fix_grem>` - implements the generalized replica exchange method
|
* :doc:`grem <fix_grem>` - implements the generalized replica exchange method
|
||||||
* :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
|
* :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
|
||||||
* :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
|
* :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
|
||||||
|
* :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
|
||||||
* :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
|
* :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
|
||||||
* :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
|
* :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
|
||||||
* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
|
* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
|
||||||
@ -258,7 +261,8 @@ accelerated styles exist.
|
|||||||
* :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
|
* :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
|
||||||
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
|
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
|
||||||
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
|
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
|
||||||
* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as driver for a quantum code via the MolSSI Driver Interface (MDI)
|
* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
|
||||||
|
* :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
|
||||||
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
|
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
|
||||||
* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
|
* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
|
||||||
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
|
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
|
||||||
@ -414,6 +418,7 @@ accelerated styles exist.
|
|||||||
* :doc:`wall/lj1043 <fix_wall>` - Lennard-Jones 10--4--3 wall
|
* :doc:`wall/lj1043 <fix_wall>` - Lennard-Jones 10--4--3 wall
|
||||||
* :doc:`wall/lj126 <fix_wall>` - Lennard-Jones 12--6 wall
|
* :doc:`wall/lj126 <fix_wall>` - Lennard-Jones 12--6 wall
|
||||||
* :doc:`wall/lj93 <fix_wall>` - Lennard-Jones 9--3 wall
|
* :doc:`wall/lj93 <fix_wall>` - Lennard-Jones 9--3 wall
|
||||||
|
* :doc:`wall/lepton <fix_wall>` - Custom Lepton expression wall
|
||||||
* :doc:`wall/morse <fix_wall>` - Morse potential wall
|
* :doc:`wall/morse <fix_wall>` - Morse potential wall
|
||||||
* :doc:`wall/piston <fix_wall_piston>` - moving reflective piston wall
|
* :doc:`wall/piston <fix_wall_piston>` - moving reflective piston wall
|
||||||
* :doc:`wall/reflect <fix_wall_reflect>` - reflecting wall(s)
|
* :doc:`wall/reflect <fix_wall_reflect>` - reflecting wall(s)
|
||||||
@ -421,6 +426,7 @@ accelerated styles exist.
|
|||||||
* :doc:`wall/region <fix_wall_region>` - use region surface as wall
|
* :doc:`wall/region <fix_wall_region>` - use region surface as wall
|
||||||
* :doc:`wall/region/ees <fix_wall_ees>` - use region surface as wall for ellipsoidal particles
|
* :doc:`wall/region/ees <fix_wall_ees>` - use region surface as wall for ellipsoidal particles
|
||||||
* :doc:`wall/srd <fix_wall_srd>` - slip/no-slip wall for SRD particles
|
* :doc:`wall/srd <fix_wall_srd>` - slip/no-slip wall for SRD particles
|
||||||
|
* :doc:`wall/table <fix_wall>` - Tabulated potential wall wall
|
||||||
* :doc:`widom <fix_widom>` - Widom insertions of atoms or molecules
|
* :doc:`widom <fix_widom>` - Widom insertions of atoms or molecules
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
|
|||||||
@ -133,13 +133,15 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
|
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`born/gauss <pair_born_gauss>` | biga0,biga1,r0 | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`buck, buck/coul/cut <pair_buck>` | a,c | type pairs |
|
| :doc:`buck, buck/coul/cut <pair_buck>` | a,c | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | a,c,coulombic_cutoff | type pairs |
|
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | a,c,coulombic_cutoff | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
| :doc:`coul/cut, coul/cut/global <pair_coul>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
@ -151,10 +153,16 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
|
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`coul/slater/long <pair_coul_slater>` | scale | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`coul/streitz <pair_coul>` | scale | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`eam, eam/alloy, eam/fs <pair_eam>` | scale | type pairs |
|
| :doc:`eam, eam/alloy, eam/fs <pair_eam>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`harmonic/cut <pair_harmonic_cut>` | k, cutoff | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`lennard/mdf <pair_mdf>` | A,B | type pairs |
|
| :doc:`lennard/mdf <pair_mdf>` | A,B | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||||
@ -181,6 +189,8 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`lubricate <pair_lubricate>` | mu | global |
|
| :doc:`lubricate <pair_lubricate>` | mu | global |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`meam <pair_meam>` | scale | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs |
|
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | D0,R0,alpha | type pairs |
|
| :doc:`morse, morse/smooth/linear <pair_morse>` | D0,R0,alpha | type pairs |
|
||||||
@ -191,7 +201,7 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
|
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`reaxff <pair_reaxff>` | chi, eta, gamma | type global |
|
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`snap <pair_snap>` | scale | type pairs |
|
| :doc:`snap <pair_snap>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
@ -203,11 +213,13 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
|
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`table <pair_table>` | table_cutoff | type pairs |
|
| :doc:`table <pair_table>` | table_cutoff | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
|
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
| :doc:`wf/cut <pair_wf_cut>` | epsilon,sigma,nu,mu | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|||||||
173
doc/src/fix_alchemy.rst
Normal file
173
doc/src/fix_alchemy.rst
Normal file
@ -0,0 +1,173 @@
|
|||||||
|
.. index:: fix alchemy
|
||||||
|
|
||||||
|
fix alchemy command
|
||||||
|
===================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
fix ID group-ID alchemy v_name
|
||||||
|
|
||||||
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
|
* alchemy = style name of this fix command
|
||||||
|
* v_name = variable with name that determines the :math:`\lambda_R` value
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix trans all alchemy v_ramp
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
This fix command enables an "alchemical transformation" to be performed
|
||||||
|
between two systems, whereby one system slowly transforms into the other
|
||||||
|
over the course of a molecular dynamics run. This is useful for
|
||||||
|
measuring thermodynamic differences between two different systems. It
|
||||||
|
also allows transformations that are not easily possible with the
|
||||||
|
:doc:`pair style hybrid/scaled <pair_hybrid>`, :doc:`fix adapt
|
||||||
|
<fix_adapt>` or :doc:`fix adapt/fep <fix_adapt_fep>` commands.
|
||||||
|
|
||||||
|
Example inputs are included in the ``examples/PACKAGES/alchemy``
|
||||||
|
directory for (a) transforming a pure copper system into a
|
||||||
|
copper/aluminum bronze alloy and (b) transforming two water molecules
|
||||||
|
in a box of water into a hydronium and a hydroxyl ion.
|
||||||
|
|
||||||
|
The two systems must be defined as :doc:`separate replica
|
||||||
|
<Howto_replica>` and run in separate partitions of processors using the
|
||||||
|
:doc:`-partition <Run_options>` command-line switch. Exactly two
|
||||||
|
partitions must be specified, and each partition must use the same number
|
||||||
|
of processors and the same domain decomposition.
|
||||||
|
|
||||||
|
Because the forces applied to the atoms are the same mix of the forces
|
||||||
|
from each partition and the simulation starts with the same atom
|
||||||
|
positions across both partitions, they will generate the same trajectory
|
||||||
|
of coordinates for each atom, and the same simulation box size and
|
||||||
|
shape. The latter two conditions are *enforced* by this fix; it
|
||||||
|
exchanges coordinates and box information between the replicas. This is
|
||||||
|
not strictly required, but since MD simulations are an example of a
|
||||||
|
chaotic system, even the tiniest random difference will eventually grow
|
||||||
|
exponentially into an unwanted divergence.
|
||||||
|
|
||||||
|
Otherwise, the properties of each atom (type, charge, bond and angle
|
||||||
|
partners, etc.), as well as energy and forces between interacting atoms
|
||||||
|
(pair, bond, angle styles, etc.) can be different in the two systems.
|
||||||
|
|
||||||
|
This can be initialized in the same input script by using commands which
|
||||||
|
only apply to one or the other replica. The example scripts use a
|
||||||
|
world-style :doc:`variable <variable>` command along with
|
||||||
|
:doc:`if/then/else <if>` commands for this purpose. The
|
||||||
|
:doc:`partition <partition>` command can also be used.
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
create_box 2 box
|
||||||
|
create_atoms 1 box
|
||||||
|
pair_style eam/alloy
|
||||||
|
pair_coeff * * AlCu.eam.alloy Cu Al
|
||||||
|
|
||||||
|
# replace 5% of copper with aluminum on the second partition only
|
||||||
|
|
||||||
|
variable name world pure alloy
|
||||||
|
if "${name} == alloy" then &
|
||||||
|
"set type 1 type/fraction 2 0.05 6745234"
|
||||||
|
|
||||||
|
Both replicas must define an instance of this fix, but with a different
|
||||||
|
*v_name* variable. The named variable must be an equal-style or
|
||||||
|
equivalent :doc:`variable <variable>`. The two variables should be
|
||||||
|
defined so that one ramps *down* from 1.0 to 0.0 for the *first* replica
|
||||||
|
(*R=0*) and the other ramps *up* from 0.0 to 1.0 for the *second*
|
||||||
|
replica (*R=1*). A simple way is to do this is linearly, which can be
|
||||||
|
done using the ramp() function of the :doc:`variable <variable>`
|
||||||
|
command. You could also define a variable which returns a value between
|
||||||
|
0.0 and 1.0 as a non-linear function of the timestep. Here is a linear
|
||||||
|
example:
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
partition yes 1 variable ramp equal ramp(1.0,0.0)
|
||||||
|
partition yes 2 variable ramp equal ramp(0.0,1.0)
|
||||||
|
fix 2 all alchemy v_ramp
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
For an alchemical transformation, the two variables should sum to
|
||||||
|
exactly 1.0 at any timestep. LAMMPS does *NOT* check that this is
|
||||||
|
the case.
|
||||||
|
|
||||||
|
If you use the ``ramp()`` function to define the two variables, this fix
|
||||||
|
can easily be used across successive runs in the same input script by
|
||||||
|
ensuring each instance of the :doc:`run <run>` command specifies the
|
||||||
|
appropriate *start* or *stop* options.
|
||||||
|
|
||||||
|
At each timestep of an MD run, the two instances of this fix evaluate
|
||||||
|
their respective variables as a :math:`\lambda_R` factor, where *R* = 0
|
||||||
|
or 1 for each replica. The forces used by each system for the
|
||||||
|
propagation of their atoms is set to the sum of the forces for the two
|
||||||
|
systems, each scaled by their respective :math:`\lambda_R` factor. Thus,
|
||||||
|
during the MD run, the system will transform incrementally from the
|
||||||
|
first system to the second system.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
As mentioned above, the coordinates of the atoms and box size/shape
|
||||||
|
must be exactly the same in the two replicas. Therefore, it is
|
||||||
|
generally not a good idea to initialize the two replicas by reading
|
||||||
|
different data files or creating them individually from scratch.
|
||||||
|
Rather, a single system should be initialized and then desired
|
||||||
|
modifications applied to the system to either replica. If your
|
||||||
|
input script somehow induces the two systems to become different
|
||||||
|
(e.g. by performing :doc:`atom_modify sort <atom_modify>`
|
||||||
|
differently, or by adding or depositing a different number of atoms),
|
||||||
|
then LAMMPS will detect the mismatch and generate an error. This is
|
||||||
|
done by ensuring that each step the number and ordering of atoms is
|
||||||
|
identical within each pair of processors in the two replicas.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
This fix stores a global scalar (the current value of :math:`\lambda_R`)
|
||||||
|
and a global vector of length 3 which contains the potential energy of
|
||||||
|
the first partition, the second partition and the combined value,
|
||||||
|
respectively. The global scalar is unitless and "intensive", the vector
|
||||||
|
is in :doc:`energy units <units>` and "extensive". These values can be
|
||||||
|
used by any command that uses a global value from a fix as input. See
|
||||||
|
the :doc:`output howto <Howto_output>` page for an overview of LAMMPS
|
||||||
|
output options.
|
||||||
|
|
||||||
|
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This fix is part of the REPLICA package. It is only enabled if LAMMPS
|
||||||
|
was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
|
There may be only one instance of this fix in use at a time within
|
||||||
|
each replica.
|
||||||
|
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`compute pressure/alchemy <compute_pressure_alchemy>` command,
|
||||||
|
:doc:`fix adapt <fix_adapt>` command, :doc:`fix adapt/fep <fix_adapt_fep>`
|
||||||
|
command, :doc:`pair_style hybrid/scaled <pair_hybrid>` command.
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
@ -15,7 +15,7 @@ Syntax
|
|||||||
* Nevery = use input values every this many time steps
|
* Nevery = use input values every this many time steps
|
||||||
* Nfreq = save state of the time correlation functions every this many time steps
|
* Nfreq = save state of the time correlation functions every this many time steps
|
||||||
* one or more input values can be listed
|
* one or more input values can be listed
|
||||||
* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name, v_name[I]
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -24,6 +24,7 @@ Syntax
|
|||||||
f_ID = global scalar calculated by a fix with ID
|
f_ID = global scalar calculated by a fix with ID
|
||||||
f_ID[I] = Ith component of global vector calculated by a fix with ID
|
f_ID[I] = Ith component of global vector calculated by a fix with ID
|
||||||
v_name = global value calculated by an equal-style variable with name
|
v_name = global value calculated by an equal-style variable with name
|
||||||
|
v_name[I] = Ith component of global vector calculated by a vector-style variable with name
|
||||||
|
|
||||||
* zero or more keyword/arg pairs may be appended
|
* zero or more keyword/arg pairs may be appended
|
||||||
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
|
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
|
||||||
|
|||||||
@ -43,6 +43,7 @@ Syntax
|
|||||||
name = name of the atom-style variable
|
name = name of the atom-style variable
|
||||||
*store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
|
*store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
|
||||||
name = atom property name (without d\_ prefix)
|
name = atom property name (without d\_ prefix)
|
||||||
|
*sort* arg = *no* or *yes*
|
||||||
*out* arg = filename
|
*out* arg = filename
|
||||||
filename = write each processor's subdomain to a file, at each re-balancing
|
filename = write each processor's subdomain to a file, at each re-balancing
|
||||||
|
|
||||||
@ -308,6 +309,14 @@ in that sub-box.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
The *sort* keyword determines whether the communication of per-atom
|
||||||
|
data to other processors during load-balancing will be random or
|
||||||
|
deterministic. Random is generally faster; deterministic will ensure
|
||||||
|
the new ordering of atoms on each processor is the same each time the
|
||||||
|
same simulation is run. This can be useful for debugging purposes.
|
||||||
|
Since the fix balance command is performed during timestepping, the
|
||||||
|
default is *no* so that sorting is not performed.
|
||||||
|
|
||||||
The *out* keyword writes text to the specified *filename* with the
|
The *out* keyword writes text to the specified *filename* with the
|
||||||
results of each re-balancing operation. The file contains the bounds
|
results of each re-balancing operation. The file contains the bounds
|
||||||
of the subdomain for each processor after the balancing operation
|
of the subdomain for each processor after the balancing operation
|
||||||
@ -415,4 +424,4 @@ Related commands
|
|||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
none
|
The default setting is sort = no.
|
||||||
|
|||||||
@ -220,11 +220,11 @@ ignored if the *global* or *local* keywords are used, since those
|
|||||||
options choose a z-coordinate for insertion independently.
|
options choose a z-coordinate for insertion independently.
|
||||||
|
|
||||||
The vx, vy, and vz components of velocity for the inserted particle
|
The vx, vy, and vz components of velocity for the inserted particle
|
||||||
are set using the values specified for the *vx*, *vy*, and *vz*
|
are set by sampling a uniform distribution between the bounds set by
|
||||||
keywords. Note that normally, new particles should be a assigned a
|
the values specified for the *vx*, *vy*, and *vz* keywords. Note that
|
||||||
negative vertical velocity so that they move towards the surface. For
|
normally, new particles should be a assigned a negative vertical
|
||||||
molecules, the same velocity is given to every particle (no rotation
|
velocity so that they move towards the surface. For molecules, the
|
||||||
or bond vibration).
|
same velocity is given to every particle (no rotation or bond vibration).
|
||||||
|
|
||||||
If the *target* option is used, the velocity vector of the inserted
|
If the *target* option is used, the velocity vector of the inserted
|
||||||
particle is changed so that it points from the insertion position
|
particle is changed so that it points from the insertion position
|
||||||
|
|||||||
@ -1,17 +1,21 @@
|
|||||||
.. index:: fix efield
|
.. index:: fix efield
|
||||||
|
.. index:: fix efield/tip4p
|
||||||
|
|
||||||
fix efield command
|
fix efield command
|
||||||
==================
|
==================
|
||||||
|
|
||||||
|
fix efield/tip4p command
|
||||||
|
========================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
fix ID group-ID efield ex ey ez keyword value ...
|
fix ID group-ID style ex ey ez keyword value ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* efield = style name of this fix command
|
* style = *efield* or *efield/tip4p*
|
||||||
* ex,ey,ez = E-field component values (electric field units)
|
* ex,ey,ez = E-field component values (electric field units)
|
||||||
* any of ex,ey,ez can be a variable (see below)
|
* any of ex,ey,ez can be a variable (see below)
|
||||||
* zero or more keyword/value pairs may be appended to args
|
* zero or more keyword/value pairs may be appended to args
|
||||||
@ -31,27 +35,36 @@ Examples
|
|||||||
|
|
||||||
fix kick external-field efield 1.0 0.0 0.0
|
fix kick external-field efield 1.0 0.0 0.0
|
||||||
fix kick external-field efield 0.0 0.0 v_oscillate
|
fix kick external-field efield 0.0 0.0 v_oscillate
|
||||||
|
fix kick external-field efield/tip4p 1.0 0.0 0.0
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
Add a force F = qE to each charged atom in the group due to an
|
Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
|
||||||
external electric field being applied to the system. If the system
|
external electric field being applied to the system. If the system
|
||||||
contains point-dipoles, also add a torque on the dipoles due to the
|
contains point-dipoles, also add a torque on the dipoles due to the
|
||||||
external electric field.
|
external electric field.
|
||||||
|
|
||||||
For charges, any of the 3 quantities defining the E-field components
|
.. versionadded:: 28Mar2023
|
||||||
can be specified as an equal-style or atom-style
|
|
||||||
:doc:`variable <variable>`, namely *ex*, *ey*, *ez*\ . If the value is a
|
When the *efield/tip4p* style is used, the E-field will be applied to
|
||||||
variable, it should be specified as v_name, where name is the variable
|
the position of the virtual charge site M of a TIP4P molecule instead of
|
||||||
name. In this case, the variable will be evaluated each timestep, and
|
the oxygen position as it is defined by a corresponding :doc:`TIP4P pair
|
||||||
its value used to determine the E-field component.
|
style <pair_lj_cut_tip4p>`. The forces on the M site due to the
|
||||||
|
external field are projected on the oxygen and hydrogen atoms of the
|
||||||
|
TIP4P molecules.
|
||||||
|
|
||||||
|
For charges, any of the 3 quantities defining the E-field components can
|
||||||
|
be specified as an equal-style or atom-style :doc:`variable <variable>`,
|
||||||
|
namely *ex*, *ey*, *ez*\ . If the value is a variable, it should be
|
||||||
|
specified as v_name, where name is the variable name. In this case, the
|
||||||
|
variable will be evaluated each timestep, and its value used to
|
||||||
|
determine the E-field component.
|
||||||
|
|
||||||
For point-dipoles, equal-style variables can be used, but atom-style
|
For point-dipoles, equal-style variables can be used, but atom-style
|
||||||
variables are not currently supported, since they imply a spatial
|
variables are not currently supported, since they imply a spatial
|
||||||
gradient in the electric field which means additional terms with
|
gradient in the electric field which means additional terms with
|
||||||
gradients of the field are required for the force and torque on
|
gradients of the field are required for the force and torque on dipoles.
|
||||||
dipoles.
|
|
||||||
|
|
||||||
Equal-style variables can specify formulas with various mathematical
|
Equal-style variables can specify formulas with various mathematical
|
||||||
functions, and include :doc:`thermo_style <thermo_style>` command
|
functions, and include :doc:`thermo_style <thermo_style>` command
|
||||||
@ -81,10 +94,18 @@ self-consistent minimization problem (see below).
|
|||||||
The *energy* keyword is not allowed if the added field is a constant
|
The *energy* keyword is not allowed if the added field is a constant
|
||||||
vector (ex,ey,ez), with all components defined as numeric constants
|
vector (ex,ey,ez), with all components defined as numeric constants
|
||||||
and not as variables. This is because LAMMPS can compute the energy
|
and not as variables. This is because LAMMPS can compute the energy
|
||||||
for each charged particle directly as E = -x dot qE = -q (x\*ex + y\*ey
|
for each charged particle directly as
|
||||||
+ z\*ez), so that -Grad(E) = F. Similarly for point-dipole particles
|
|
||||||
the energy can be computed as E = -mu dot E = -(mux\*ex + muy\*ey +
|
.. math::
|
||||||
muz\*ez).
|
|
||||||
|
U_{efield} = -\vec{x} \cdot q\vec{E} = -q (x\cdot E_x + y\cdot E_y + z\cdot Ez),
|
||||||
|
|
||||||
|
so that :math:`-\nabla U_{efield} = \vec{F}`. Similarly for point-dipole particles
|
||||||
|
the energy can be computed as
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
U_{efield} = -\vec{\mu} \cdot \vec{E} = -\mu_x\cdot E_x + \mu_y\cdot E_y + \mu_z\cdot E_z
|
||||||
|
|
||||||
The *energy* keyword is optional if the added force is defined with
|
The *energy* keyword is optional if the added force is defined with
|
||||||
one or more variables, and if you are performing dynamics via the
|
one or more variables, and if you are performing dynamics via the
|
||||||
@ -120,29 +141,28 @@ Restart, fix_modify, output, run start/stop, minimize info
|
|||||||
No information about this fix is written to :doc:`binary restart files
|
No information about this fix is written to :doc:`binary restart files
|
||||||
<restart>`.
|
<restart>`.
|
||||||
|
|
||||||
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
|
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
|
||||||
this fix to add the potential energy inferred by the added force due
|
fix to add the potential energy inferred by the added force due to the
|
||||||
to the electric field to the global potential energy of the system as
|
electric field to the global potential energy of the system as part of
|
||||||
part of :doc:`thermodynamic output <thermo_style>`. The default
|
:doc:`thermodynamic output <thermo_style>`. The default setting for
|
||||||
setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
|
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
|
||||||
Note that this energy is a fictitious quantity but is needed so that
|
energy is a fictitious quantity but is needed so that the :doc:`minimize
|
||||||
the :doc:`minimize <minimize>` command can include the forces added by
|
<minimize>` command can include the forces added by this fix in a
|
||||||
this fix in a consistent manner. I.e. there is a decrease in
|
consistent manner. I.e. there is a decrease in potential energy when
|
||||||
potential energy when atoms move in the direction of the added force
|
atoms move in the direction of the added force due to the electric
|
||||||
due to the electric field.
|
field.
|
||||||
|
|
||||||
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
|
||||||
this fix to add the contribution due to the added forces on atoms to
|
fix to add the contribution due to the added forces on atoms to both the
|
||||||
both the global pressure and per-atom stress of the system via the
|
global pressure and per-atom stress of the system via the :doc:`compute
|
||||||
:doc:`compute pressure <compute_pressure>` and :doc:`compute
|
pressure <compute_pressure>` and :doc:`compute stress/atom
|
||||||
stress/atom <compute_stress_atom>` commands. The former can be
|
<compute_stress_atom>` commands. The former can be accessed by
|
||||||
accessed by :doc:`thermodynamic output <thermo_style>`. The default
|
:doc:`thermodynamic output <thermo_style>`. The default setting for
|
||||||
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
|
this fix is :doc:`fix_modify virial no <fix_modify>`.
|
||||||
|
|
||||||
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
|
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
|
||||||
fix. This allows to set at which level of the :doc:`r-RESPA
|
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
|
||||||
<run_style>` integrator the fix adding its forces. Default is the
|
integrator the fix adding its forces. Default is the outermost level.
|
||||||
outermost level.
|
|
||||||
|
|
||||||
This fix computes a global scalar and a global 3-vector of forces,
|
This fix computes a global scalar and a global 3-vector of forces,
|
||||||
which can be accessed by various :doc:`output commands
|
which can be accessed by various :doc:`output commands
|
||||||
@ -169,7 +189,11 @@ the iteration count during the minimization.
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
None
|
Fix style *efield/tip4p* 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.
|
||||||
|
|
||||||
|
Fix style *efield/tip4p* can only be used with tip4p pair styles.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
70
doc/src/fix_heat_flow.rst
Normal file
70
doc/src/fix_heat_flow.rst
Normal file
@ -0,0 +1,70 @@
|
|||||||
|
.. index:: fix heat/flow
|
||||||
|
|
||||||
|
fix heat/flow command
|
||||||
|
==========================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
fix ID group-ID heat/flow style values ...
|
||||||
|
|
||||||
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
|
* heat/flow = style name of this fix command
|
||||||
|
* one style with corresponding value(s) needs to be listed
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
style = *constant* or *type*
|
||||||
|
*constant* = cp
|
||||||
|
cp = value of specifc heat (energy/(mass * temperature) units)
|
||||||
|
*type* = cp1 ... cpN
|
||||||
|
cpN = value of specifc heat for type N (energy/(mass * temperature) units)
|
||||||
|
|
||||||
|
*
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix 1 all heat/flow constant 1.0
|
||||||
|
fix 1 all heat/flow type 1.0 0.5
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
Perform plain time integration to update temperature for atoms in the
|
||||||
|
group each timestep. The specific heat of atoms can be defined using either
|
||||||
|
the *constant* or *type* keywords. For style *constant*, the specific heat
|
||||||
|
is a constant value *cp* for all atoms. For style *type*, *N* different values
|
||||||
|
of the specific heat are defined, one for each of the *N* types of atoms.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
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 global or per-atom quantities are stored by this fix for access by various
|
||||||
|
:doc:`output commands <Howto_output>`. 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>`.
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This fix requires that atoms store temperature and heat flow
|
||||||
|
as defined by the :doc:`fix property/atom <fix_property_atom>` command.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
@ -8,12 +8,12 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
fix ID group-ID mdi/qm keyword
|
fix ID group-ID mdi/qm keyword value(s) keyword value(s) ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* mdi/qm = style name of this fix command
|
* mdi/qm = style name of this fix command
|
||||||
* zero or more keyword/value pairs may be appended
|
* zero or more keyword/value pairs may be appended
|
||||||
* keyword = *virial* or *add* or *every* or *connect* or *elements*
|
* keyword = *virial* or *add* or *every* or *connect* or *elements* or *mc*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -29,7 +29,9 @@ Syntax
|
|||||||
yes = perform a one-time connection to the MDI engine code
|
yes = perform a one-time connection to the MDI engine code
|
||||||
no = do not perform the connection operation
|
no = do not perform the connection operation
|
||||||
*elements* args = N_1 N_2 ... N_ntypes
|
*elements* args = N_1 N_2 ... N_ntypes
|
||||||
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
|
||||||
|
*mc* args = mcfixID
|
||||||
|
mcfixID = ID of a Monte Carlo fix designed to work with this fix
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -38,7 +40,7 @@ Examples
|
|||||||
|
|
||||||
fix 1 all mdi/qm
|
fix 1 all mdi/qm
|
||||||
fix 1 all mdi/qm virial yes
|
fix 1 all mdi/qm virial yes
|
||||||
fix 1 all mdi/qm add no every 100 elements 13 29
|
fix 1 all mdi/qm add no every 100 elements C C H O
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -57,12 +59,27 @@ The server code must support use of the `MDI Library
|
|||||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
||||||
explained below.
|
explained below.
|
||||||
|
|
||||||
|
Typically, to use this fix, the input script should not define any
|
||||||
|
other classical force field components, e.g. a pair style, bond style,
|
||||||
|
etc.
|
||||||
|
|
||||||
These are example use cases for this fix, discussed further below:
|
These are example use cases for this fix, discussed further below:
|
||||||
|
|
||||||
* perform an ab initio MD (AIMD) simulation with quantum forces
|
* perform an ab initio MD (AIMD) simulation with quantum forces
|
||||||
* perform an energy minimization with quantum forces
|
* perform an energy minimization with quantum forces
|
||||||
* perform a nudged elastic band (NEB) calculation with quantum forces
|
* perform a nudged elastic band (NEB) calculation with quantum forces
|
||||||
* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
|
* perform a QM calculation for a series of independent systems which
|
||||||
|
LAMMPS reads or generates once
|
||||||
|
* run a classical MD simulation and calculate QM energy/forces once
|
||||||
|
every N steps on the current configuration
|
||||||
|
|
||||||
|
More generally any command which calculates per-atom forces can instead
|
||||||
|
use quantum forces by defining this fix. Examples are the Monte Carlo
|
||||||
|
commands :doc:`fix gcmc <fix_gcmc>` and :doc:`fix atom/swap
|
||||||
|
<fix_atom_swap>`, as well as the :doc:`compute born/matrix
|
||||||
|
<compute_born_matrix>` command. The only requirement is that internally
|
||||||
|
the command invokes the post_force() method of fixes such as this one,
|
||||||
|
which will trigger the quantum calculation.
|
||||||
|
|
||||||
The code coupling performed by this command is done via the `MDI
|
The code coupling performed by this command is done via the `MDI
|
||||||
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
||||||
@ -72,27 +89,32 @@ for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
|
|||||||
information about how LAMMPS can operate as either an MDI driver or
|
information about how LAMMPS can operate as either an MDI driver or
|
||||||
engine.
|
engine.
|
||||||
|
|
||||||
The examples/mdi directory contains input scripts using this fix in
|
The ``examples/mdi`` directory contains input scripts using this fix in
|
||||||
the various use cases discussed below. In each case, two instances of
|
the various use cases discussed below. In each case, two instances of
|
||||||
LAMMPS are used, once as an MDI driver, once as an MDI engine
|
LAMMPS are used, once as an MDI driver, once as an MDI engine (surrogate
|
||||||
(surrogate for a QM code). The examples/mdi/README file explains how
|
for a QM code). The ``examples/mdi/README`` file explains how to launch
|
||||||
to launch two codes so that they communicate via the MDI library using
|
two codes so that they communicate via the MDI library using either MPI
|
||||||
either MPI or sockets. Any QM code that supports MDI could be used in
|
or sockets. Any QM code that supports MDI could be used in place of
|
||||||
place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi
|
LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi <Howto_mdi>`
|
||||||
<Howto_mdi>` page for a current list (March 2022) of such QM codes.
|
page for a current list (March 2022) of such QM codes. The
|
||||||
|
``examples/QUANTUM`` directory has examples for coupling LAMMPS to 3 QM
|
||||||
|
codes either via this fix or the :doc:`fix mdi/qmmm <fix_mdi_qmmm>`
|
||||||
|
command.
|
||||||
|
|
||||||
Note that an engine code can support MDI in either or both of two
|
Note that an engine code can support MDI in either or both of two modes.
|
||||||
modes. It can be used as a stand-alone code, launched at the same
|
It can be used as a stand-alone code, launched at the same time as
|
||||||
time as LAMMPS. Or it can be used as a plugin library, which LAMMPS
|
LAMMPS. Or it can be used as a plugin library, which LAMMPS loads. See
|
||||||
loads. See the :doc:`mdi plugin <mdi>` command for how to trigger
|
the :doc:`mdi plugin <mdi>` command for how to trigger LAMMPS to load a
|
||||||
LAMMPS to load a plugin library. The examples/mdi/README file
|
plugin library. The ``examples/mdi/README`` file and
|
||||||
explains how to launch the two codes in either mode.
|
``examples/QUANTUM/QM-code/README`` files explain how to launch the two
|
||||||
|
codes in either mode.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The *virial* keyword setting of yes or no determines whether
|
The *virial* keyword setting of yes or no determines whether LAMMPS
|
||||||
LAMMPS will request the QM code to also compute and return
|
will request the QM code to also compute and return the QM
|
||||||
a 6-element symmetric virial tensor for the system.
|
contribution to a stress tensor for the system which LAMMPS will
|
||||||
|
convert to a 6-element symmetric virial tensor.
|
||||||
|
|
||||||
The *add* keyword setting of *yes* or *no* determines whether the
|
The *add* keyword setting of *yes* or *no* determines whether the
|
||||||
energy and forces and virial returned by the QM code will be added to
|
energy and forces and virial returned by the QM code will be added to
|
||||||
@ -109,25 +131,27 @@ commands. See details below.
|
|||||||
The *every* keyword determines how often the QM code will be invoked
|
The *every* keyword determines how often the QM code will be invoked
|
||||||
during a dynamics run with the current LAMMPS simulation box and
|
during a dynamics run with the current LAMMPS simulation box and
|
||||||
configuration of atoms. The QM code will be called once every
|
configuration of atoms. The QM code will be called once every
|
||||||
*Nevery* timesteps.
|
*Nevery* timesteps. By default *Nevery* = 1.
|
||||||
|
|
||||||
The *connect* keyword determines whether this fix performs a one-time
|
The *connect* keyword determines whether this fix performs a one-time
|
||||||
connection to the QM code. The default is *yes*. The only time a
|
connection to the QM code. The default is *yes*. The only time a *no*
|
||||||
*no* is needed is if this command is used multiple times in an input
|
is needed is if this command is used multiple times in an input script
|
||||||
script. E.g. if it used inside a loop which also uses the :doc:`clear
|
and the MDI coupling is between two stand-alone codes (not plugin mode).
|
||||||
<clear>` command to destroy the system (including any defined fixes).
|
E.g. if it used inside a loop which also uses the :doc:`clear <clear>`
|
||||||
See the examples/mdi/in.series.driver script as an example of this,
|
command to destroy the system (including this fix). See the
|
||||||
where LAMMPS is using the QM code to compute energy and forces for a
|
``examples/mdi/in.series.driver`` script as an example of this, where
|
||||||
series of system configurations. In this use case *connect no*
|
LAMMPS is using the QM code to compute energy and forces for a series of
|
||||||
is used along with the :doc:`mdi connect and exit <mdi>` command
|
system configurations. In this use case *connect no* is used along with
|
||||||
to one-time initiate/terminate the connection outside the loop.
|
the :doc:`mdi connect and exit <mdi>` command to one-time
|
||||||
|
initiate/terminate the connection outside the loop.
|
||||||
|
|
||||||
The *elements* keyword allows specification of what element each
|
The *elements* keyword allows specification of what element each
|
||||||
LAMMPS atom type corresponds to. This is specified by the atomic
|
LAMMPS atom type corresponds to. This is specified by the chemical
|
||||||
number of the element, e.g. 13 for Al. An atomic number must be
|
symbol of the element, e.g. C or Al or Si. A symbol must be specified
|
||||||
specified for each of the ntypes LAMMPS atom types. Ntypes is
|
for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
|
||||||
typically specified via the create_box command or in the data file
|
represent the same element. Ntypes is typically specified via the
|
||||||
read by the read_data command.
|
:doc:`create_box <create_box>` command or in the data file read by the
|
||||||
|
:doc:`read_data <read_data>` command.
|
||||||
|
|
||||||
If this keyword is specified, then this fix will send the MDI
|
If this keyword is specified, then this fix will send the MDI
|
||||||
">ELEMENTS" command to the engine, to ensure the two codes are
|
">ELEMENTS" command to the engine, to ensure the two codes are
|
||||||
@ -136,10 +160,18 @@ not specified, then this fix will send the MDI >TYPES command to the
|
|||||||
engine. This is fine if both the LAMMPS driver and the MDI engine are
|
engine. This is fine if both the LAMMPS driver and the MDI engine are
|
||||||
initialized so that the atom type values are consistent in both codes.
|
initialized so that the atom type values are consistent in both codes.
|
||||||
|
|
||||||
|
The *mc* keyword enables this fix to be used with a Monte Carlo (MC)
|
||||||
|
fix to calculate before/after quantum energies as part of the MC
|
||||||
|
accept/reject criterion. The :doc:`fix gcmc <fix_gcmc>` and :doc:`fix
|
||||||
|
atom/swap <fix_atom_swap>` commands can be used in this manner.
|
||||||
|
Specify the ID of the MC fix following the *mc* keyword. This allows
|
||||||
|
the two fixes to coordinate when MC events are being calculated versus
|
||||||
|
MD timesteps between the MC events.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The following 3 example use cases are illustrated in the examples/mdi
|
The following 3 example use cases are illustrated in the
|
||||||
directory. See its README file for more details.
|
``examples/mdi`` directory. See its README file for more details.
|
||||||
|
|
||||||
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
|
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
|
||||||
minimization with QM forces, or a multi-replica NEB calculation, use
|
minimization with QM forces, or a multi-replica NEB calculation, use
|
||||||
@ -252,12 +284,6 @@ This command is part of the MDI package. It is only enabled if
|
|||||||
LAMMPS was built with that package. See the :doc:`Build package
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
<Build_package>` page for more info.
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
The QM code does not currently compute and return per-atom energy or
|
|
||||||
per-atom virial contributions. So they will not show up as part of
|
|
||||||
the calculations performed by the :doc:`compute pe/atom
|
|
||||||
<compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>`
|
|
||||||
commands.
|
|
||||||
|
|
||||||
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
||||||
codes (MD or QM codes), the :doc:`units <units>` command should be
|
codes (MD or QM codes), the :doc:`units <units>` command should be
|
||||||
used to specify *real* or *metal* units. This will ensure the correct
|
used to specify *real* or *metal* units. This will ensure the correct
|
||||||
@ -265,12 +291,15 @@ unit conversions between LAMMPS and MDI units. The other code will
|
|||||||
also perform similar unit conversions into its preferred units.
|
also perform similar unit conversions into its preferred units.
|
||||||
|
|
||||||
LAMMPS can also be used as an MDI driver in other unit choices it
|
LAMMPS can also be used as an MDI driver in other unit choices it
|
||||||
supports, e.g. *lj*, but then no unit conversion is performed.
|
supports, e.g. *lj*, but then no unit conversion to MDI units is
|
||||||
|
performed.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`mdi plugin <mdi>`, :doc:`mdi engine <mdi>`
|
:doc:`mdi plugin <mdi>`,
|
||||||
|
:doc:`mdi engine <mdi>`,
|
||||||
|
:doc:`fix mdi/qmmm <fix_mdi_qmmm>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
274
doc/src/fix_mdi_qmmm.rst
Normal file
274
doc/src/fix_mdi_qmmm.rst
Normal file
@ -0,0 +1,274 @@
|
|||||||
|
.. index:: fix mdi/qmmm
|
||||||
|
|
||||||
|
fix mdi/qmmm command
|
||||||
|
====================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
fix ID group-ID mdi/qmmm mode keyword value(s) keyword value(s) ...
|
||||||
|
|
||||||
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
|
* mdi/qmmm = style name of this fix command
|
||||||
|
* mode = *direct* or *potential*
|
||||||
|
* zero or more keyword/value pairs may be appended
|
||||||
|
* keyword = *virial* or *add* or *every* or *connect* or *elements*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
*virial* args = *yes* or *no*
|
||||||
|
yes = request virial tensor from server code
|
||||||
|
no = do not request virial tensor from server code
|
||||||
|
*connect* args = *yes* or *no*
|
||||||
|
yes = perform a one-time connection to the MDI engine code
|
||||||
|
no = do not perform the connection operation
|
||||||
|
*elements* args = N_1 N_2 ... N_ntypes
|
||||||
|
N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix 1 all mdi/qmmm direct
|
||||||
|
fix 1 all mdi/qmmm potential virial yes
|
||||||
|
fix 1 all mdi/qmmm potential virial yes elements 13 29
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
This command enables LAMMPS to act as a client with another server code
|
||||||
|
to perform a coupled QM/MM (quantum-mechanics/molecular-mechanics)
|
||||||
|
simulation. LAMMPS will perform classical MD (molecular mechanics
|
||||||
|
or MM) for the (typically larger) MM portion of the system. A quantum
|
||||||
|
mechanics code will calculate quantum energy and forces for the QM
|
||||||
|
portion of the system. The two codes work together to calculate the
|
||||||
|
energy and forces due to the cross interactions between QM and MM atoms.
|
||||||
|
The QM server code must support use of the `MDI Library
|
||||||
|
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
||||||
|
explained below.
|
||||||
|
|
||||||
|
The partitioning of the system between QM and MM atoms is as follows.
|
||||||
|
Atoms in the specified group are QM atoms; the remaining atoms are MM
|
||||||
|
atoms. The input script should thus define this partitioning.
|
||||||
|
See additional information below about other requirements for an input
|
||||||
|
script to use this fix and perform a QM/MM simulation.
|
||||||
|
|
||||||
|
The code coupling performed by this command is done via the `MDI
|
||||||
|
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
||||||
|
LAMMPS runs as an MDI driver (client), and sends MDI commands to an
|
||||||
|
external MDI engine code (server), in this case a QM code which has
|
||||||
|
support for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
|
||||||
|
information about how LAMMPS can operate as either an MDI driver or
|
||||||
|
engine.
|
||||||
|
|
||||||
|
The ``examples/QUANTUM`` directory has sub-directories with example
|
||||||
|
input scripts using this fix in tandem with different QM codes. The
|
||||||
|
README files in the sub-directories explain how to download and build
|
||||||
|
the various QM codes. They also explain how to launch LAMMPS and the QM
|
||||||
|
code so that they communicate via the MDI library using either MPI or
|
||||||
|
sockets. Any QM code that supports MDI could be used in addition to
|
||||||
|
those discussed in the sub-directories. See the :doc:`Howto mdi
|
||||||
|
<Howto_mdi>` page for a current list (March 2022) of such QM codes.
|
||||||
|
|
||||||
|
Note that an engine code can support MDI in either or both of two modes.
|
||||||
|
It can be used as a stand-alone code, launched at the same time as
|
||||||
|
LAMMPS. Or it can be used as a plugin library, which LAMMPS loads. See
|
||||||
|
the :doc:`mdi plugin <mdi>` command for how to trigger LAMMPS to load a
|
||||||
|
plugin library. The ``examples/QUANTUM`` sub-directory README files
|
||||||
|
explains how to launch the two codes in either mode.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The *mode* setting determines which QM/MM coupling algorithm is used.
|
||||||
|
LAMMPS currently supports *direct* and *potential* algorithms, based
|
||||||
|
on the *mode* setting. Both algorithms should give reasonably
|
||||||
|
accurate results, but some QM codes support only one of the two modes.
|
||||||
|
E.g. in the ``examples/QUANTUM`` directory, PySCF supports only *direct*,
|
||||||
|
NWChem supports only *potential*, and LATTE currently supports
|
||||||
|
neither, so it cannot be used for QM/MM simulations using this fix.
|
||||||
|
|
||||||
|
The *direct* option passes the coordinates and charges of each MM atom
|
||||||
|
to the quantum code, in addition to the coordinates of each QM atom.
|
||||||
|
The quantum code returns forces on each QM atom as well as forces on
|
||||||
|
each MM atom. The latter is effectively the force on MM atoms due to
|
||||||
|
the QM atoms.
|
||||||
|
|
||||||
|
The input script for performing a *direct* mode QM/MM simulation should
|
||||||
|
do the following:
|
||||||
|
|
||||||
|
* delete all bonds (angles, dihedrals, etc) between QM atoms
|
||||||
|
* set the charge on each QM atom to zero
|
||||||
|
* define no bonds (angles, dihedrals, etc) which involve both QM and MM atoms
|
||||||
|
* define a force field (pair, bonds, angles, optional kspace) for the entire system
|
||||||
|
|
||||||
|
The first two bullet can be performed using the :doc:`delete_bonds
|
||||||
|
<delete_bonds>` and :doc:`set <set>` commands.
|
||||||
|
|
||||||
|
The third bullet is required to have a consistent model, but is not
|
||||||
|
checked by LAMMPS.
|
||||||
|
|
||||||
|
The fourth bullet implies that non-bonded non-Coulombic interactions
|
||||||
|
(e.g. van der Waals) between QM/QM and QM/MM pairs of atoms are
|
||||||
|
computed by LAMMPS.
|
||||||
|
|
||||||
|
See the ``examples/QUANTUM/PySCF/in.*`` files for examples of input
|
||||||
|
scripts for QM/MM simulations using the *direct* mode.
|
||||||
|
|
||||||
|
The *potential* option passes the coordinates of each QM atom and a
|
||||||
|
Coulomb potential for each QM atom to the quantum code. The latter is
|
||||||
|
calculated by performing a Coulombics-only calculation for the entire
|
||||||
|
system, subtracting all QM/QM pairwise Coulombic terms, and dividing
|
||||||
|
the Coulomb energy on each QM atom by the charge of the QM atom. The
|
||||||
|
potential value represents the Coulombic influence of all the MM atoms
|
||||||
|
on each QM atom.
|
||||||
|
|
||||||
|
The quantum code returns forces and charge on each QM atom. The new
|
||||||
|
charges on the QM atom are used to re-calculate the MM force field,
|
||||||
|
resulting in altered forces on the MM atoms.
|
||||||
|
|
||||||
|
The input script for performing a *potential* mode QM/MM simulation
|
||||||
|
should do the following:
|
||||||
|
|
||||||
|
* delete all bonds (angles, dihedrals, etc) between QM atoms
|
||||||
|
* define a hybrid pair style which includes a Coulomb-only pair sub-style
|
||||||
|
* define no bonds (angles, dihedrals, etc) which involve both QM and MM atoms
|
||||||
|
* define a force field (pair, bonds, angles, optional kspace) for the entire system
|
||||||
|
|
||||||
|
The first operation can be performed using the :doc:`delete_bonds
|
||||||
|
<delete_bonds>` command. See the ``examples/QUANTUM/NWChem/in.*`` files
|
||||||
|
for examples of how to do this.
|
||||||
|
|
||||||
|
The second operation is necessary so that this fix can calculate the
|
||||||
|
Coulomb potential for the QM atoms.
|
||||||
|
|
||||||
|
The third bullet is required to have a consistent model, but is not
|
||||||
|
checked by LAMMPS.
|
||||||
|
|
||||||
|
The fourth bullet implies that non-bonded non-Coulombic interactions
|
||||||
|
(e.g. van der Waals) between QM/QM and QM/MM pairs of atoms are computed
|
||||||
|
by LAMMPS. However, some QM codes do not want the MM code (LAMMPS) to
|
||||||
|
compute QM/QM van der Waals interactions. NWChem is an example. In
|
||||||
|
this case, the coefficients for those interactions need to be turned
|
||||||
|
off, which typically requires the atom types for the QM atoms be
|
||||||
|
different than those for the MM atoms.
|
||||||
|
|
||||||
|
See the ``examples/QUANTUM/NWChem/in.*`` files for examples of input
|
||||||
|
scripts for QM/MM simulations using the *potential* mode. Those scripts
|
||||||
|
also illustrate how to turn off QM/QM van der Waals interactions.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The *virial* keyword setting of yes or no determines whether LAMMPS
|
||||||
|
will request the QM code to also compute and return the QM
|
||||||
|
contribution to a stress tensor for the system which LAMMPS will
|
||||||
|
convert to a 6-element symmetric virial tensor.
|
||||||
|
|
||||||
|
The *connect* keyword determines whether this fix performs a one-time
|
||||||
|
connection to the QM code. The default is *yes*. The only time a
|
||||||
|
*no* is needed is if this command is used multiple times in an input
|
||||||
|
script. E.g. if it used inside a loop which also uses the :doc:`clear
|
||||||
|
<clear>` command to destroy the system (including this fix). As
|
||||||
|
example would be a script which loop over a series of independent QM/MM
|
||||||
|
simulations, e.g. each with their own data file. In this use case
|
||||||
|
*connect no* could be used along with the :doc:`mdi connect and exit
|
||||||
|
<mdi>` command to one-time initiate/terminate the connection outside
|
||||||
|
the loop.
|
||||||
|
|
||||||
|
The *elements* keyword allows specification of what element each
|
||||||
|
LAMMPS atom type corresponds to. This is specified by the chemical
|
||||||
|
symbol of the element, e.g. C or Al or Si. A symbol must be specified
|
||||||
|
for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
|
||||||
|
represent the same element. Ntypes is typically specified via the
|
||||||
|
:doc:`create_box <create_box>` command or in the data file read by the
|
||||||
|
:doc:`read_data <read_data>` command.
|
||||||
|
|
||||||
|
If this keyword is specified, then this fix will send the MDI
|
||||||
|
">ELEMENTS" command to the engine, to insure the two codes are
|
||||||
|
consistent in their definition of atomic species. If this keyword is
|
||||||
|
not specified, then this fix will send the MDI >TYPES command to the
|
||||||
|
engine. This is fine if both the LAMMPS driver and the MDI engine are
|
||||||
|
initialized so that the atom type values are consistent in both codes.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
No information about this fix is written to :doc:`binary restart files
|
||||||
|
<restart>`.
|
||||||
|
|
||||||
|
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
|
||||||
|
this fix to add the potential energy computed by the QM code to the
|
||||||
|
global potential energy of the system as part of :doc:`thermodynamic
|
||||||
|
output <thermo_style>`. The default setting for this fix is
|
||||||
|
:doc:`fix_modify energy yes <fix_modify>`.
|
||||||
|
|
||||||
|
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||||
|
this fix to add the contribution computed by the QM code to the global
|
||||||
|
pressure of the system as part of :doc:`thermodynamic output
|
||||||
|
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
|
||||||
|
virial yes <fix_modify>`.
|
||||||
|
|
||||||
|
This fix computes a global scalar which can be accessed by various
|
||||||
|
:doc:`output commands <Howto_output>`. The scalar is the energy
|
||||||
|
returned by the QM code. The scalar value calculated by this fix is
|
||||||
|
"extensive".
|
||||||
|
|
||||||
|
This fix also computes a global vector with of length 6 which contains
|
||||||
|
the symmetric virial tensor values returned by the QM code. It can
|
||||||
|
likewise be accessed by various :doc:`output commands <Howto_output>`.
|
||||||
|
|
||||||
|
The ordering of values in the symmetric virial tensor is as follows:
|
||||||
|
vxx, vyy, vzz, vxy, vxz, vyz. The values will be in pressure
|
||||||
|
:doc:`units <units>`.
|
||||||
|
|
||||||
|
This fix also computes a peratom array with 3 columns which contains
|
||||||
|
the peratom forces returned by the QM code. It can likewise be
|
||||||
|
accessed by various :doc:`output commands <Howto_output>`. Note that
|
||||||
|
for *direct* mode this will be quantum forces on both QM and MM atoms.
|
||||||
|
For *potential* mode it will only be quantum forces on QM atoms; the
|
||||||
|
forces for MM atoms will be zero.
|
||||||
|
|
||||||
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
|
the :doc:`run <run>` command.
|
||||||
|
|
||||||
|
The forces computed by the QM code are used during an energy
|
||||||
|
minimization, invoked by the :doc:`minimize <minimize>` command.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
If you want the potential energy associated with the QM forces to
|
||||||
|
be included in the total potential energy of the system (the
|
||||||
|
quantity being minimized), you MUST not disable the
|
||||||
|
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
|
||||||
|
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This command is part of the MDI package. It is only enabled if
|
||||||
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
|
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
||||||
|
codes (MD or QM codes), the :doc:`units <units>` command should be
|
||||||
|
used to specify *real* or *metal* units. This will ensure the correct
|
||||||
|
unit conversions between LAMMPS and MDI units. The other code will
|
||||||
|
also perform similar unit conversions into its preferred units.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`mdi plugin <mdi>`,
|
||||||
|
:doc:`mdi engine <mdi>`,
|
||||||
|
:doc:`fix mdi/qm <fix_mdi_qm>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
The default for the optional keywords are virial = no and connect = yes.
|
||||||
@ -40,15 +40,15 @@ Description
|
|||||||
|
|
||||||
This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
|
This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
|
||||||
snapshots from a dump file to generate potentials for coarse-grained
|
snapshots from a dump file to generate potentials for coarse-grained
|
||||||
simulations from all-atom simulations, using a force-matching
|
simulations from all-atom simulations, using a force-matching technique
|
||||||
technique (:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
|
(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
|
||||||
|
|
||||||
It makes use of the MS-CG library, written and maintained by Greg
|
It makes use of the MS-CG library, written and maintained by Greg Voth's
|
||||||
Voth's group at the University of Chicago, which is freely available
|
group at the University of Chicago, which is freely available on their
|
||||||
on their `MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_. See instructions
|
`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
|
||||||
on obtaining and installing the MS-CG library in the src/MSCG/README
|
See instructions on obtaining and installing the MS-CG library in the
|
||||||
file, which must be done before you build LAMMPS with this fix command
|
src/MSCG/README file, which must be done before you build LAMMPS with
|
||||||
and use the command in a LAMMPS input script.
|
this fix command and use the command in a LAMMPS input script.
|
||||||
|
|
||||||
An example script using this fix is provided the examples/mscg
|
An example script using this fix is provided the examples/mscg
|
||||||
directory.
|
directory.
|
||||||
@ -65,15 +65,18 @@ simulations is as follows:
|
|||||||
6. Check the results of the force matching.
|
6. Check the results of the force matching.
|
||||||
7. Run coarse-grained simulations using the new coarse-grained potentials.
|
7. Run coarse-grained simulations using the new coarse-grained potentials.
|
||||||
|
|
||||||
This fix can perform the range finding and force matching steps 4 and
|
This fix can perform the range finding and force matching steps 4 and 5
|
||||||
5 of the above workflow when used in conjunction with the
|
of the above workflow when used in conjunction with the :doc:`rerun
|
||||||
:doc:`rerun <rerun>` command. It does not perform steps 1-3 and 6-7.
|
<rerun>` command. It does not perform steps 1-3 and 6-7.
|
||||||
|
|
||||||
Step 2 can be performed using a Python script (what is the name?)
|
Step 2 can be performed using a Python script (cgmap), which defines the
|
||||||
provided with the MS-CG library which defines the coarse-grained model
|
coarse-grained model and converts a standard LAMMPS dump file for an
|
||||||
and converts a standard LAMMPS dump file for an all-atom simulation
|
all-atom simulation (step 1) into a LAMMPS dump file which has the
|
||||||
(step 1) into a LAMMPS dump file which has the positions of and forces
|
positions of and forces on the coarse-grained beads. To use cgmap the
|
||||||
on the coarse-grained beads.
|
following repositories need to be downloaded and installed.
|
||||||
|
|
||||||
|
#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
|
||||||
|
#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
|
||||||
|
|
||||||
In step 3, an input file named "control.in" is needed by the MS-CG
|
In step 3, an input file named "control.in" is needed by the MS-CG
|
||||||
library which sets parameters for the range finding and force matching
|
library which sets parameters for the range finding and force matching
|
||||||
@ -83,12 +86,12 @@ info on this file.
|
|||||||
|
|
||||||
When this fix is used to perform steps 4 and 5, the MS-CG library also
|
When this fix is used to perform steps 4 and 5, the MS-CG library also
|
||||||
produces additional output files. The range finder functionality
|
produces additional output files. The range finder functionality
|
||||||
(step 4) outputs files defining pair and bonded interaction ranges.
|
(step 4) outputs files defining pair and bonded interaction ranges. The
|
||||||
The force matching functionality (step 5) outputs tabulated force
|
force matching functionality (step 5) outputs tabulated force files for
|
||||||
files for every interaction in the system. Other diagnostic files can
|
every interaction in the system. Other diagnostic files can also be
|
||||||
also be output depending on the parameters in the MS-CG library input
|
output depending on the parameters in the MS-CG library input script.
|
||||||
script. Again, see the documentation provided with the MS-CG library
|
Again, see the documentation provided with the MS-CG library for more
|
||||||
for more info.
|
info.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -97,8 +100,8 @@ be invoked. If *on*, the step 4 range finder functionality is invoked.
|
|||||||
*off*, the step 5 force matching functionality is invoked.
|
*off*, the step 5 force matching functionality is invoked.
|
||||||
|
|
||||||
If the *name* keyword is used, string names are defined to associate
|
If the *name* keyword is used, string names are defined to associate
|
||||||
with the integer atom types in LAMMPS. *Ntype* names must be
|
with the integer atom types in LAMMPS. *Ntype* names must be provided,
|
||||||
provided, one for each atom type (1-Ntype).
|
one for each atom type (1-Ntype).
|
||||||
|
|
||||||
The *max* keyword specifies the maximum number of bonds, angles, and
|
The *max* keyword specifies the maximum number of bonds, angles, and
|
||||||
dihedrals a bead can have in the coarse-grained model.
|
dihedrals a bead can have in the coarse-grained model.
|
||||||
@ -107,16 +110,13 @@ Restrictions
|
|||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This fix is part of the MSCG package. It is only enabled if LAMMPS was
|
This fix is part of the MSCG package. It is only enabled if LAMMPS was
|
||||||
built with that package. See the :doc:`Build package <Build_package>`
|
built with that package. Building the MSCG package also requires
|
||||||
doc page for more info.
|
external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
|
||||||
|
pages for more info.
|
||||||
The MS-CG library uses C++11, which may not be supported by older
|
|
||||||
compilers. The MS-CG library also has some additional numeric library
|
|
||||||
dependencies, which are described in its documentation.
|
|
||||||
|
|
||||||
Currently, the MS-CG library is not set up to run in parallel with MPI,
|
Currently, the MS-CG library is not set up to run in parallel with MPI,
|
||||||
so this fix can only be used in a serial LAMMPS build and run
|
so this fix can only be used in a serial LAMMPS build and run on a
|
||||||
on a single processor.
|
single processor.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -65,33 +65,37 @@ a default value of 0.5 is used, which effectively reproduces the
|
|||||||
standard velocity-Verlet (VV) scheme. For more details, see
|
standard velocity-Verlet (VV) scheme. For more details, see
|
||||||
:ref:`Groot <Groot2>`.
|
:ref:`Groot <Groot2>`.
|
||||||
|
|
||||||
Fix *mvv/dpd* updates the position and velocity of each atom. It can
|
Fix *mvv/dpd* updates the position and velocity of each atom. It can be
|
||||||
be used with the :doc:`pair_style mdpd <pair_mesodpd>` command or other
|
used with the :doc:`pair_style mdpd <pair_mesodpd>` command or other
|
||||||
pair styles such as :doc:`pair dpd <pair_dpd>`.
|
pair styles such as :doc:`pair dpd <pair_dpd>`.
|
||||||
|
|
||||||
Fix *mvv/edpd* updates the per-atom temperature, in addition to
|
Fix *mvv/edpd* updates the per-atom temperature, in addition to position
|
||||||
position and velocity, and must be used with the :doc:`pair_style edpd <pair_mesodpd>` command.
|
and velocity, and must be used with the :doc:`pair_style edpd
|
||||||
|
<pair_mesodpd>` command.
|
||||||
|
|
||||||
Fix *mvv/tdpd* updates the per-atom chemical concentration, in
|
Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition
|
||||||
addition to position and velocity, and must be used with the
|
to position and velocity, and must be used with the :doc:`pair_style
|
||||||
:doc:`pair_style tdpd <pair_mesodpd>` command.
|
tdpd <pair_mesodpd>` command.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
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
|
No information about this fix is written to :doc:`binary restart files
|
||||||
are relevant to this fix. No global or per-atom quantities are stored
|
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
|
||||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
relevant to this fix. No global or per-atom quantities are stored by
|
||||||
|
this fix for access by various :doc:`output commands <Howto_output>`.
|
||||||
No parameter of this fix can be used with the *start/stop* keywords of
|
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
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This fix is part of the DPD-MESO package. It is only enabled if
|
These fixes are part of the DPD-MESO package. They are only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -218,10 +218,11 @@ use :doc:`change_box <change_box>` before invoking the fix.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
|
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`,
|
||||||
:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
|
:doc:`fix nvt/sllod <fix_nvt_sllod>`,
|
||||||
:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
|
:doc:`compute temp/uef <compute_temp_uef>`,
|
||||||
:doc:<dump_cfg_uef>`
|
:doc:`compute pressure/uef <compute_pressure_uef>`,
|
||||||
|
:doc:`dump cfg/uef <dump_cfg_uef>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: fix pimd/nvt
|
.. index:: fix pimd/nvt
|
||||||
|
|
||||||
fix pimd/nvt command
|
fix pimd/nvt command
|
||||||
================
|
====================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
@ -33,7 +33,7 @@ Examples
|
|||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
.. versionchanged:: TBD
|
.. versionchanged:: 28Mar2023
|
||||||
|
|
||||||
Fix pimd was renamed to fix pimd/nvt.
|
Fix pimd was renamed to fix pimd/nvt.
|
||||||
|
|
||||||
|
|||||||
@ -31,7 +31,7 @@ Examples
|
|||||||
|
|
||||||
fix 2 interface polarize/bem/gmres 5 0.0001
|
fix 2 interface polarize/bem/gmres 5 0.0001
|
||||||
fix 1 interface polarize/bem/icc 1 0.0001
|
fix 1 interface polarize/bem/icc 1 0.0001
|
||||||
fix 3 interface polarize/functional 1 0.001
|
fix 3 interface polarize/functional 1 0.0001
|
||||||
|
|
||||||
|
|
||||||
Used in input scripts:
|
Used in input scripts:
|
||||||
@ -69,8 +69,9 @@ along the normal vector is then 78 - 4 = 74, the mean dielectric value
|
|||||||
is (78 + 4) / 2 = 41. Each boundary element also has its area and the
|
is (78 + 4) / 2 = 41. Each boundary element also has its area and the
|
||||||
local mean curvature, which is used by these fixes for computing a
|
local mean curvature, which is used by these fixes for computing a
|
||||||
correction term in the local electric field. To model charged
|
correction term in the local electric field. To model charged
|
||||||
interfaces, the interface particle will have a non-zero charge value,
|
interfaces, an interface particle will have a non-zero charge value,
|
||||||
coming from its area and surface charge density.
|
coming from its area and surface charge density, and its local dielectric
|
||||||
|
constant set to the mean dielectric value.
|
||||||
|
|
||||||
For non-interface particles such as atoms and charged particles, the
|
For non-interface particles such as atoms and charged particles, the
|
||||||
interface normal vectors, element area, and dielectric mismatch are
|
interface normal vectors, element area, and dielectric mismatch are
|
||||||
@ -211,6 +212,8 @@ Note that the *polarize/bem/gmres* and *polarize/bem/icc* fixes only
|
|||||||
support :doc:`units <units>` *lj*, *real*, *metal*, *si* and *nano* at
|
support :doc:`units <units>` *lj*, *real*, *metal*, *si* and *nano* at
|
||||||
the moment.
|
the moment.
|
||||||
|
|
||||||
|
Note that *polarize/functional* does not yet support charged interfaces.
|
||||||
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
@ -223,7 +226,7 @@ Related commands
|
|||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
*iter_max* = 20
|
*iter_max* = 50
|
||||||
|
|
||||||
*kspace* = yes
|
*kspace* = yes
|
||||||
|
|
||||||
|
|||||||
@ -61,7 +61,7 @@ unchanged and controlling the pressure of a surrounding fluid.
|
|||||||
atoms. This fix can be used in conjunction with thermostatting fixes
|
atoms. This fix can be used in conjunction with thermostatting fixes
|
||||||
to control the temperature, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen <fix_temp_berendsen>`.
|
to control the temperature, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen <fix_temp_berendsen>`.
|
||||||
|
|
||||||
See the :doc:`Howto baroostat <Howto_barostat>` page for a
|
See the :doc:`Howto barostat <Howto_barostat>` page for a
|
||||||
discussion of different ways to perform barostatting.
|
discussion of different ways to perform barostatting.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|||||||
@ -63,7 +63,7 @@ however, can *only* be applied during molecular dynamics runs.
|
|||||||
|
|
||||||
.. versionchanged:: 15Sep2022
|
.. versionchanged:: 15Sep2022
|
||||||
|
|
||||||
These fixes may still be used during minimization. In that case the
|
These fixes may now also be used during minimization. In that case the
|
||||||
constraints are *approximated* by strong harmonic restraints.
|
constraints are *approximated* by strong harmonic restraints.
|
||||||
|
|
||||||
**SHAKE vs RATTLE:**
|
**SHAKE vs RATTLE:**
|
||||||
@ -133,9 +133,9 @@ constraint lists atom types. All bonds connected to an atom of the
|
|||||||
specified type will be constrained. The *m* constraint lists atom
|
specified type will be constrained. The *m* constraint lists atom
|
||||||
masses. All bonds connected to atoms of the specified masses will be
|
masses. All bonds connected to atoms of the specified masses will be
|
||||||
constrained (within a fudge factor of MASSDELTA specified in
|
constrained (within a fudge factor of MASSDELTA specified in
|
||||||
fix_shake.cpp). The *a* constraint lists angle types. If both bonds
|
``src/RIGID/fix_shake.cpp``). The *a* constraint lists angle types. If
|
||||||
in the angle are constrained then the angle will also be constrained
|
both bonds in the angle are constrained then the angle will also be
|
||||||
if its type is in the list.
|
constrained if its type is in the list.
|
||||||
|
|
||||||
For all constraints, a particular bond is only constrained if both
|
For all constraints, a particular bond is only constrained if both
|
||||||
atoms in the bond are in the group specified with the SHAKE fix.
|
atoms in the bond are in the group specified with the SHAKE fix.
|
||||||
@ -205,11 +205,11 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
|
|||||||
The *fix rattle* command modifies forces and velocities and thus
|
The *fix rattle* command modifies forces and velocities and thus
|
||||||
should be defined after all other integration fixes in your input
|
should be defined after all other integration fixes in your input
|
||||||
script. If you define other fixes that modify velocities or forces
|
script. If you define other fixes that modify velocities or forces
|
||||||
after *fix rattle* operates, then *fix rattle* will not take them into
|
after *fix rattle* operates, then *fix rattle* will not take them
|
||||||
account and the overall time integration will typically not satisfy
|
into account and the overall time integration will typically not
|
||||||
the RATTLE constraints. You can check whether the constraints work
|
satisfy the RATTLE constraints. You can check whether the
|
||||||
correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
|
constraints work correctly by setting the value of RATTLE_DEBUG in
|
||||||
to 1 and recompiling LAMMPS.
|
``src/RIGID/fix_rattle.cpp`` to 1 and recompiling LAMMPS.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -275,8 +275,8 @@ reducing the :doc:`timestep <timestep>`.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
`fix rigid <fix_rigid>`, `fix ehex <fix_ehex>`,
|
:doc:`fix rigid <fix_rigid>`, :doc:`fix ehex <fix_ehex>`,
|
||||||
`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
|
:doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
|
||||||
|
|
||||||
|
|
||||||
Default
|
Default
|
||||||
|
|||||||
@ -4,7 +4,9 @@
|
|||||||
.. index:: fix wall/lj1043
|
.. index:: fix wall/lj1043
|
||||||
.. index:: fix wall/colloid
|
.. index:: fix wall/colloid
|
||||||
.. index:: fix wall/harmonic
|
.. index:: fix wall/harmonic
|
||||||
|
.. index:: fix wall/lepton
|
||||||
.. index:: fix wall/morse
|
.. index:: fix wall/morse
|
||||||
|
.. index:: fix wall/table
|
||||||
|
|
||||||
fix wall/lj93 command
|
fix wall/lj93 command
|
||||||
=====================
|
=====================
|
||||||
@ -23,20 +25,31 @@ fix wall/colloid command
|
|||||||
fix wall/harmonic command
|
fix wall/harmonic command
|
||||||
=========================
|
=========================
|
||||||
|
|
||||||
|
fix wall/lepton command
|
||||||
|
=========================
|
||||||
|
|
||||||
fix wall/morse command
|
fix wall/morse command
|
||||||
======================
|
======================
|
||||||
|
|
||||||
|
fix wall/table command
|
||||||
|
=========================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
fix ID group-ID style face args ... keyword value ...
|
fix ID group-ID style [tabstyle] [N] face args ... keyword value ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* or *wall/morse*
|
* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* or *wall/lepton* or *wall/morse* or *wall/table*
|
||||||
|
* tabstyle = *linear* or *spline* = method of table interpolation (only applies to *wall/table*)
|
||||||
|
* N = use N values in *linear* or *spline* interpolation (only applies to *wall/table*)
|
||||||
* one or more face/arg pairs may be appended
|
* one or more face/arg pairs may be appended
|
||||||
* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
|
* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
|
||||||
|
|
||||||
|
.. spacer
|
||||||
|
|
||||||
* args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic*
|
* args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
@ -50,7 +63,19 @@ Syntax
|
|||||||
epsilon can be a variable (see below)
|
epsilon can be a variable (see below)
|
||||||
sigma = size factor for wall-particle interaction (distance units)
|
sigma = size factor for wall-particle interaction (distance units)
|
||||||
sigma can be a variable (see below)
|
sigma can be a variable (see below)
|
||||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
|
cutoff = distance from wall at which wall-particle interactions are cut off (distance units)
|
||||||
|
|
||||||
|
* args for style *lepton*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
args = coord expression cutoff
|
||||||
|
coord = position of wall = EDGE or constant or variable
|
||||||
|
EDGE = current lo or hi edge of simulation box
|
||||||
|
constant = number like 0.0 or -30.0 (distance units)
|
||||||
|
variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
|
||||||
|
expression = Lepton expression for the potential (energy units)
|
||||||
|
cutoff = distance from wall at which wall-particle interactions are cut off (distance units)
|
||||||
|
|
||||||
* args for style *morse*
|
* args for style *morse*
|
||||||
|
|
||||||
@ -67,7 +92,20 @@ Syntax
|
|||||||
alpha can be a variable (see below)
|
alpha can be a variable (see below)
|
||||||
r_0 = distance of the potential minimum from the face of region (distance units)
|
r_0 = distance of the potential minimum from the face of region (distance units)
|
||||||
r_0 can be a variable (see below)
|
r_0 can be a variable (see below)
|
||||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
|
cutoff = distance from wall at which wall-particle interactions are cut off (distance units)
|
||||||
|
|
||||||
|
* args for style *table*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
args = coord filename keyword cutoff
|
||||||
|
coord = position of wall = EDGE or constant or variable
|
||||||
|
EDGE = current lo or hi edge of simulation box
|
||||||
|
constant = number like 0.0 or -30.0 (distance units)
|
||||||
|
variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
|
||||||
|
filename = file containing tabulated energy and force values
|
||||||
|
keyword = section identifier to select a specific table in table file
|
||||||
|
cutoff = distance from wall at which wall-particle interactions are cut off (distance units)
|
||||||
|
|
||||||
* zero or more keyword/value pairs may be appended
|
* zero or more keyword/value pairs may be appended
|
||||||
* keyword = *units* or *fld* or *pbc*
|
* keyword = *units* or *fld* or *pbc*
|
||||||
@ -91,9 +129,13 @@ Examples
|
|||||||
|
|
||||||
fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
|
fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
|
||||||
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
|
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
|
||||||
|
fix wallhi all wall/harmonic xhi EDGE 100.0 0.0 4.0 units box
|
||||||
fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
|
fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
|
||||||
fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
|
fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
|
||||||
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
|
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
|
||||||
|
fix xwall mobile wall/table spline 200 EDGE -5.0 walltab.dat HARMONIC 4.0
|
||||||
|
fix xwalls mobile wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0
|
||||||
|
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -103,7 +145,7 @@ wall that interacts with the atoms in the group by generating a force
|
|||||||
on the atom in a direction perpendicular to the wall. The energy of
|
on the atom in a direction perpendicular to the wall. The energy of
|
||||||
wall-particle interactions depends on the style.
|
wall-particle interactions depends on the style.
|
||||||
|
|
||||||
For style *wall/lj93*, the energy E is given by the 9/3 potential:
|
For style *wall/lj93*, the energy E is given by the 9-3 Lennard-Jones potential:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -111,7 +153,7 @@ For style *wall/lj93*, the energy E is given by the 9/3 potential:
|
|||||||
\left(\frac{\sigma}{r}\right)^3 \right]
|
\left(\frac{\sigma}{r}\right)^3 \right]
|
||||||
\qquad r < r_c
|
\qquad r < r_c
|
||||||
|
|
||||||
For style *wall/lj126*, the energy E is given by the 12/6 potential:
|
For style *wall/lj126*, the energy E is given by the 12-6 Lennard-Jones potential:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -119,7 +161,7 @@ For style *wall/lj126*, the energy E is given by the 12/6 potential:
|
|||||||
\left(\frac{\sigma}{r}\right)^6 \right]
|
\left(\frac{\sigma}{r}\right)^6 \right]
|
||||||
\qquad r < r_c
|
\qquad r < r_c
|
||||||
|
|
||||||
For style *wall/lj1043*, the energy E is given by the 10/4/3 potential:
|
For style *wall/lj1043*, the energy E is given by the 10-4-3 Lennard-Jones potential:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -138,8 +180,8 @@ of the :doc:`pair_style colloid <pair_colloid>` potential:
|
|||||||
& \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
|
& \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
|
||||||
\left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c
|
\left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c
|
||||||
|
|
||||||
For style *wall/harmonic*, the energy E is given by a harmonic spring
|
For style *wall/harmonic*, the energy E is given by a repulsive-only harmonic
|
||||||
potential:
|
spring potential:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -152,6 +194,60 @@ For style *wall/morse*, the energy E is given by a Morse potential:
|
|||||||
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
|
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
|
||||||
\qquad r < r_c
|
\qquad r < r_c
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
For style *wall/lepton*, the energy E is provided as an Lepton
|
||||||
|
expression string using "r" as the distance variable. The `Lepton
|
||||||
|
library <https://simtk.org/projects/lepton>`_, that the *wall/lepton*
|
||||||
|
style interfaces with, evaluates this expression string at run time to
|
||||||
|
compute the wall-particle energy. It also creates an analytical
|
||||||
|
representation of the first derivative of this expression with respect
|
||||||
|
to "r" and then uses that to compute the force between the wall and
|
||||||
|
atoms in the fix group. The Lepton expression must be either enclosed
|
||||||
|
in quotes or must not contain any whitespace so that LAMMPS recognizes
|
||||||
|
it as a single keyword.
|
||||||
|
|
||||||
|
Optionally, the expression may use "rc" to refer to the cutoff distance
|
||||||
|
for the given wall. Further constants in the expression can be defined
|
||||||
|
in the same string as additional expressions separated by semi-colons.
|
||||||
|
The expression "k*(r-rc)^2;k=100.0" represents a repulsive-only harmonic
|
||||||
|
spring as in fix *wall/harmonic* with a force constant *K* (same as
|
||||||
|
:math:`\epsilon` above) of 100 energy units. More details on the Lepton
|
||||||
|
expression strings are given below.
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
For style *wall/table*, the energy E and forces are determined from
|
||||||
|
interpolation tables listed in one or more files as a function of
|
||||||
|
distance. The interpolation tables are used to evaluate energy and
|
||||||
|
forces between particles and the wall similar to how analytic formulas
|
||||||
|
are used for the other wall styles.
|
||||||
|
|
||||||
|
The interpolation tables are created as a pre-computation by fitting
|
||||||
|
cubic splines to the file values and interpolating energy and force
|
||||||
|
values at each of *N* distances. During a simulation, the tables are
|
||||||
|
used to interpolate energy and force values as needed for each wall and
|
||||||
|
particle separated by a distance *R*\ . The interpolation is done in
|
||||||
|
one of two styles: *linear* or *spline*\ .
|
||||||
|
|
||||||
|
For the *linear* style, the distance *R* is used to find the 2
|
||||||
|
surrounding table values from which an energy or force is computed by
|
||||||
|
linear interpolation.
|
||||||
|
|
||||||
|
For the *spline* style, cubic spline coefficients are computed and
|
||||||
|
stored for each of the *N* values in the table, one set of splines for
|
||||||
|
energy, another for force. Note that these splines are different than
|
||||||
|
the ones used to pre-compute the *N* values. Those splines were fit
|
||||||
|
to the *Nfile* values in the tabulated file, where often *Nfile* <
|
||||||
|
*N*\ . The distance *R* is used to find the appropriate set of spline
|
||||||
|
coefficients which are used to evaluate a cubic polynomial which
|
||||||
|
computes the energy or force.
|
||||||
|
|
||||||
|
For each wall a filename and a keyword must be provided as in the
|
||||||
|
examples above. The filename specifies a file containing tabulated
|
||||||
|
energy and force values. The keyword specifies a section of the file.
|
||||||
|
The format of this file is described below.
|
||||||
|
|
||||||
In all cases, *r* is the distance from the particle to the wall at
|
In all cases, *r* is the distance from the particle to the wall at
|
||||||
position *coord*, and :math:`r_c` is the *cutoff* distance at which the
|
position *coord*, and :math:`r_c` is the *cutoff* distance at which the
|
||||||
particle and wall no longer interact. The energy of the wall
|
particle and wall no longer interact. The energy of the wall
|
||||||
@ -180,11 +276,12 @@ box parameters and timestep and elapsed time. Thus it is easy to
|
|||||||
specify a time-dependent wall position. See examples below.
|
specify a time-dependent wall position. See examples below.
|
||||||
|
|
||||||
For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
|
For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
|
||||||
:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones parameters, which
|
:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones
|
||||||
determine the strength and size of the particle as it interacts with
|
parameters, which determine the strength and size of the particle as it
|
||||||
the wall. Epsilon has energy units. Note that this :math:`\epsilon` and
|
interacts with the wall. Epsilon has energy units. Note that this
|
||||||
:math:`\sigma` may be different than any :math:`\epsilon` or :math:`\sigma` values defined
|
:math:`\epsilon` and :math:`\sigma` may be different than any
|
||||||
for a pair style that computes particle-particle interactions.
|
:math:`\epsilon` or :math:`\sigma` values defined for a pair style that
|
||||||
|
computes particle-particle interactions.
|
||||||
|
|
||||||
The *wall/lj93* interaction is derived by integrating over a 3d
|
The *wall/lj93* interaction is derived by integrating over a 3d
|
||||||
half-lattice of Lennard-Jones 12/6 particles. The *wall/lj126*
|
half-lattice of Lennard-Jones 12/6 particles. The *wall/lj126*
|
||||||
@ -207,11 +304,11 @@ are the number density of the constituent particles, in the wall and
|
|||||||
colloid respectively, in units of 1/volume.
|
colloid respectively, in units of 1/volume.
|
||||||
|
|
||||||
The *wall/colloid* interaction is derived by integrating over
|
The *wall/colloid* interaction is derived by integrating over
|
||||||
constituent LJ particles of size :math:`\sigma` within the colloid particle
|
constituent LJ particles of size :math:`\sigma` within the colloid
|
||||||
and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma`
|
particle and a 3d half-lattice of Lennard-Jones 12/6 particles of size
|
||||||
in the wall. As mentioned in the preceding paragraph, the density of
|
:math:`\sigma` in the wall. As mentioned in the preceding paragraph,
|
||||||
particles in the wall and colloid can be different, as specified by
|
the density of particles in the wall and colloid can be different, as
|
||||||
the :math:`\epsilon` prefactor.
|
specified by the :math:`\epsilon` prefactor.
|
||||||
|
|
||||||
For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
|
For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
|
||||||
constant K, and has units (energy/distance\^2). The input parameter
|
constant K, and has units (energy/distance\^2). The input parameter
|
||||||
@ -220,20 +317,21 @@ spring is at the *cutoff*\ . This is a repulsive-only spring since the
|
|||||||
interaction is truncated at the *cutoff*
|
interaction is truncated at the *cutoff*
|
||||||
|
|
||||||
For the *wall/morse* style, the three parameters are in this order:
|
For the *wall/morse* style, the three parameters are in this order:
|
||||||
:math:`D_0` the depth of the potential, :math:`\alpha` the width parameter, and
|
:math:`D_0` the depth of the potential, :math:`\alpha` the width
|
||||||
:math:`r_0` the location of the minimum. :math:`D_0` has energy units, :math:`\alpha`
|
parameter, and :math:`r_0` the location of the minimum. :math:`D_0` has
|
||||||
inverse distance units, and :math:`r_0` distance units.
|
energy units, :math:`\alpha` inverse distance units, and :math:`r_0`
|
||||||
|
distance units.
|
||||||
|
|
||||||
For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can
|
For any wall that supports them, the :math:`\epsilon` and/or
|
||||||
be specified
|
:math:`\sigma` and/or :math:`\alpha` parameter can be specified as an
|
||||||
as an :doc:`equal-style variable <variable>`, in which case it should be
|
:doc:`equal-style variable <variable>`, in which case it should be
|
||||||
specified as v_name, where name is the variable name. As with a
|
specified as v_name, where name is the variable name. As with a
|
||||||
variable wall position, the variable is evaluated each timestep and
|
variable wall position, the variable is evaluated each timestep and the
|
||||||
the result becomes the current epsilon or sigma of the wall.
|
result becomes the current epsilon or sigma of the wall. Equal-style
|
||||||
Equal-style variables can specify formulas with various mathematical
|
variables can specify formulas with various mathematical functions, and
|
||||||
functions, and include :doc:`thermo_style <thermo_style>` command
|
include :doc:`thermo_style <thermo_style>` command keywords for the
|
||||||
keywords for the simulation box parameters and timestep and elapsed
|
simulation box parameters and timestep and elapsed time. Thus it is
|
||||||
time. Thus it is easy to specify a time-dependent wall interaction.
|
easy to specify a time-dependent wall interaction.
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
@ -266,20 +364,19 @@ define the lattice spacings.
|
|||||||
The *fld* keyword can be used with a *yes* setting to invoke the wall
|
The *fld* keyword can be used with a *yes* setting to invoke the wall
|
||||||
constraint before pairwise interactions are computed. This allows an
|
constraint before pairwise interactions are computed. This allows an
|
||||||
implicit FLD model using :doc:`pair_style lubricateU <pair_lubricateU>`
|
implicit FLD model using :doc:`pair_style lubricateU <pair_lubricateU>`
|
||||||
to include the wall force in its calculations. If the setting is
|
to include the wall force in its calculations. If the setting is *no*,
|
||||||
*no*, wall forces are imposed after pairwise interactions, in the
|
wall forces are imposed after pairwise interactions, in the usual
|
||||||
usual manner.
|
manner.
|
||||||
|
|
||||||
The *pbc* keyword can be used with a *yes* setting to allow walls to
|
The *pbc* keyword can be used with a *yes* setting to allow walls to be
|
||||||
be specified in a periodic dimension. See the
|
specified in a periodic dimension. See the :doc:`boundary <boundary>`
|
||||||
:doc:`boundary <boundary>` command for options on simulation box
|
command for options on simulation box boundaries. The default for *pbc*
|
||||||
boundaries. The default for *pbc* is *no*, which means the system
|
is *no*, which means the system must be non-periodic when using a wall.
|
||||||
must be non-periodic when using a wall. But you may wish to use a
|
But you may wish to use a periodic box. E.g. to allow some particles to
|
||||||
periodic box. E.g. to allow some particles to interact with the wall
|
interact with the wall via the fix group-ID, and others to pass through
|
||||||
via the fix group-ID, and others to pass through it and wrap around a
|
it and wrap around a periodic box. In this case you should ensure that
|
||||||
periodic box. In this case you should ensure that the wall if
|
the wall is sufficiently far enough away from the box boundary. If you
|
||||||
sufficiently far enough away from the box boundary. If you do not,
|
do not, then particles may interact with both the wall and with periodic
|
||||||
then particles may interact with both the wall and with periodic
|
|
||||||
images on the other side of the box, which is probably not what you
|
images on the other side of the box, which is probably not what you
|
||||||
want.
|
want.
|
||||||
|
|
||||||
@ -328,6 +425,57 @@ perturbation on the particles:
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
.. include:: lepton_expression.rst
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Table file format
|
||||||
|
"""""""""""""""""
|
||||||
|
|
||||||
|
Suitable tables for use with fix *wall/table* can be created by the
|
||||||
|
Python code in the ``tools/tabulate`` folder of the LAMMPS source code
|
||||||
|
distribution.
|
||||||
|
|
||||||
|
The format of a tabulated file is as follows (without the parenthesized
|
||||||
|
comments):
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
# Tabulated wall potential UNITS: real
|
||||||
|
|
||||||
|
HARMONIC (keyword is the first text on a line)
|
||||||
|
N 100 FP 200 200
|
||||||
|
(blank line)
|
||||||
|
1 0.04 1568.16 792.00 (index, distance to wall, energy, force)
|
||||||
|
2 0.08 1536.64 784.00
|
||||||
|
3 0.12 1505.44 776.00
|
||||||
|
...
|
||||||
|
99 3.96 0.16 8.00
|
||||||
|
100 4.00 0 0
|
||||||
|
|
||||||
|
A section begins with a non-blank line whose first character is not a
|
||||||
|
"#"; blank lines or lines starting with "#" can be used as comments
|
||||||
|
between sections. The first line begins with a keyword which identifies
|
||||||
|
the section. The line can contain additional text, but the initial text
|
||||||
|
must match the argument specified in the fix *wall/table* command. The
|
||||||
|
next line lists (in any order) one or more parameters for the table.
|
||||||
|
Each parameter is a keyword followed by one or more numeric values.
|
||||||
|
|
||||||
|
The parameter "N" is required and its value is the number of table
|
||||||
|
entries that follow. Note that this may be different than the *N*
|
||||||
|
specified in the fix *wall/table* command. Let Ntable = *N* in the fix
|
||||||
|
command, and Nfile = "N" in the tabulated file. What LAMMPS does is a
|
||||||
|
preliminary interpolation by creating splines using the Nfile tabulated
|
||||||
|
values as nodal points. It uses these to interpolate as needed to
|
||||||
|
generate energy and force values at Ntable different points. The
|
||||||
|
resulting tables of length Ntable are then used as described above, when
|
||||||
|
computing energy and force for wall-particle interactions. This means that
|
||||||
|
if you want the interpolation tables of length Ntable to match exactly
|
||||||
|
what is in the tabulated file (with effectively no preliminary
|
||||||
|
interpolation), you should set Ntable = Nfile.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
@ -354,16 +502,15 @@ fix. This allows to set at which level of the :doc:`r-RESPA
|
|||||||
<run_style>` integrator the fix is adding its forces. Default is the
|
<run_style>` integrator the fix is adding its forces. Default is the
|
||||||
outermost level.
|
outermost level.
|
||||||
|
|
||||||
This fix computes a global scalar energy and a global vector of
|
This fix computes a global scalar energy and a global vector of forces,
|
||||||
forces, which can be accessed by various :doc:`output commands
|
which can be accessed by various :doc:`output commands <Howto_output>`.
|
||||||
<Howto_output>`. Note that the scalar energy is the sum of
|
Note that the scalar energy is the sum of interactions with all defined
|
||||||
interactions with all defined walls. If you want the energy on a
|
walls. If you want the energy on a per-wall basis, you need to use
|
||||||
per-wall basis, you need to use multiple fix wall commands. The
|
multiple fix wall commands. The length of the vector is equal to the
|
||||||
length of the vector is equal to the number of walls defined by the
|
number of walls defined by the fix. Each vector value is the normal
|
||||||
fix. Each vector value is the normal force on a specific wall. Note
|
force on a specific wall. Note that an outward force on a wall will be
|
||||||
that an outward force on a wall will be a negative value for *lo*
|
a negative value for *lo* walls and a positive value for *hi* walls.
|
||||||
walls and a positive value for *hi* walls. The scalar and vector
|
The scalar and vector values calculated by this fix are "extensive".
|
||||||
values calculated by this fix are "extensive".
|
|
||||||
|
|
||||||
No parameter of this fix can be used with the *start/stop* keywords of
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
the :doc:`run <run>` command.
|
the :doc:`run <run>` command.
|
||||||
@ -386,7 +533,11 @@ invoked by the :doc:`minimize <minimize>` command.
|
|||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
none
|
|
||||||
|
Fix *wall/lepton* is part of the LEPTON package and only enabled if
|
||||||
|
LAMMPS was built with this package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -46,7 +46,7 @@ Syntax
|
|||||||
radius = cylinder radius (distance units)
|
radius = cylinder radius (distance units)
|
||||||
|
|
||||||
* zero or more keyword/value pairs may be appended to args
|
* zero or more keyword/value pairs may be appended to args
|
||||||
* keyword = *wiggle* or *shear* or *contacts*
|
* keyword = *wiggle* or *shear* or *contacts* or *temperature*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -59,6 +59,8 @@ Syntax
|
|||||||
vshear = magnitude of shear velocity (velocity units)
|
vshear = magnitude of shear velocity (velocity units)
|
||||||
*contacts* value = none
|
*contacts* value = none
|
||||||
generate contact information for each particle
|
generate contact information for each particle
|
||||||
|
*temperature* value = temperature
|
||||||
|
specify temperature of wall
|
||||||
|
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
@ -71,7 +73,7 @@ Examples
|
|||||||
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
|
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
|
||||||
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
|
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
|
||||||
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
|
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
|
||||||
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
|
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji heat 10 region myCone temperature 1.0
|
||||||
fix 6 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
|
fix 6 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
|
||||||
|
|
||||||
Description
|
Description
|
||||||
@ -177,6 +179,16 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
|
|||||||
*vshear* < 0. In this case, *vshear* is the tangential velocity of
|
*vshear* < 0. In this case, *vshear* is the tangential velocity of
|
||||||
the wall at whatever *radius* has been defined.
|
the wall at whatever *radius* has been defined.
|
||||||
|
|
||||||
|
The *temperature* keyword is used to assign a temperature to the wall.
|
||||||
|
The following value can either be a numeric value or an equal-style
|
||||||
|
:doc:`variable <variable>`. If the value is a variable, it should be
|
||||||
|
specified as v_name, where name is the variable name. In this case, the
|
||||||
|
variable will be evaluated each timestep, and its value used to determine
|
||||||
|
the temperature. This option must be used in conjunction with a heat
|
||||||
|
conduction model defined in :doc:`pair_style granular <pair_granular>`,
|
||||||
|
:doc:`fix property/atom <fix_property_atom>` to store temperature and a
|
||||||
|
heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
|
||||||
|
flow.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|||||||
@ -36,12 +36,14 @@ Syntax
|
|||||||
|
|
||||||
* wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
|
* wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
|
||||||
* region-ID = region whose boundary will act as wall
|
* region-ID = region whose boundary will act as wall
|
||||||
* keyword = *contacts*
|
* keyword = *contacts* or *temperature*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*contacts* value = none
|
*contacts* value = none
|
||||||
generate contact information for each particle
|
generate contact information for each particle
|
||||||
|
*temperature* value = temperature
|
||||||
|
specify temperature of wall
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -200,6 +202,17 @@ values for the 6 wall/particle coefficients than for particle/particle
|
|||||||
interactions. E.g. if you wish to model the wall as a different
|
interactions. E.g. if you wish to model the wall as a different
|
||||||
material.
|
material.
|
||||||
|
|
||||||
|
The *temperature* keyword is used to assign a temperature to the wall.
|
||||||
|
The following value can either be a numeric value or an equal-style
|
||||||
|
:doc:`variable <variable>`. If the value is a variable, it should be
|
||||||
|
specified as v_name, where name is the variable name. In this case, the
|
||||||
|
variable will be evaluated each timestep, and its value used to determine
|
||||||
|
the temperature. This option must be used in conjunction with a heat
|
||||||
|
conduction model defined in :doc:`pair_style granular <pair_granular>`,
|
||||||
|
:doc:`fix property/atom <fix_property_atom>` to store temperature and a
|
||||||
|
heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
|
||||||
|
flow.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
.. index:: improper_style amoeba
|
.. index:: improper_style amoeba
|
||||||
|
|
||||||
improper_style harmonic command
|
improper_style amoeba command
|
||||||
===============================
|
=============================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
|
|||||||
@ -17,7 +17,7 @@ Syntax
|
|||||||
*engine* args = zero or more keyword/args pairs
|
*engine* args = zero or more keyword/args pairs
|
||||||
keywords = *elements*
|
keywords = *elements*
|
||||||
*elements* args = N_1 N_2 ... N_ntypes
|
*elements* args = N_1 N_2 ... N_ntypes
|
||||||
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
|
||||||
*plugin* args = name keyword value keyword value ...
|
*plugin* args = name keyword value keyword value ...
|
||||||
name = name of plugin library (e.g., *lammps* means a liblammps.so library will be loaded)
|
name = name of plugin library (e.g., *lammps* means a liblammps.so library will be loaded)
|
||||||
keyword/value pairs in any order, some are required, some are optional
|
keyword/value pairs in any order, some are required, some are optional
|
||||||
@ -35,7 +35,7 @@ Examples
|
|||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
mdi engine elements 13 29
|
mdi engine elements Al Cu
|
||||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||||
command "run 5"
|
command "run 5"
|
||||||
@ -173,13 +173,16 @@ commands, which are described further below.
|
|||||||
atom type values are consistent in both codes, then the >TYPES
|
atom type values are consistent in both codes, then the >TYPES
|
||||||
command can be used. If not, the optional *elements* keyword can
|
command can be used. If not, the optional *elements* keyword can
|
||||||
be used to specify what element each LAMMPS atom type corresponds
|
be used to specify what element each LAMMPS atom type corresponds
|
||||||
to. This is specified by the atomic number of the element (e.g., 13
|
to. This is specified by the chemical symbol of the element,
|
||||||
for Al). An atomic number must be specified for each of the ntypes
|
e.g. C or Al or Si. A symbol must be specified for each of the
|
||||||
LAMMPS atom types. Ntypes is typically specified via the
|
ntypes LAMMPS atom types. Each LAMMPS type must map to a unique
|
||||||
create_box command or in the data file read by the read_data
|
element; two or more types cannot map to the same element. Ntypes
|
||||||
command. In this has been done, the MDI driver can send an
|
is typically specified via the :doc:`create_box <create_box>`
|
||||||
>ELEMENTS command to the LAMMPS driver with the atomic number of
|
command or in the data file read by the :doc:`read_data
|
||||||
each atom.
|
<read_data>` command. Once this has been done, the MDI driver can
|
||||||
|
send an >ELEMENTS command to the LAMMPS driver with the atomic
|
||||||
|
number of each atom and the LAMMPS engine will be able to map it to
|
||||||
|
a LAMMPS atom type.
|
||||||
|
|
||||||
The MD and OPTG commands perform an entire MD simulation or energy
|
The MD and OPTG commands perform an entire MD simulation or energy
|
||||||
minimization (to convergence) with no communication from the driver
|
minimization (to convergence) with no communication from the driver
|
||||||
|
|||||||
@ -49,19 +49,19 @@ and forces) by pushing the atoms off of each other.
|
|||||||
|
|
||||||
The distance that atoms can move during individual minimization steps
|
The distance that atoms can move during individual minimization steps
|
||||||
can be quite large, especially at the beginning of a minimization.
|
can be quite large, especially at the beginning of a minimization.
|
||||||
Thus `neighbor list settings <neigh_modify>` of *every = 1* and
|
Thus :doc:`neighbor list settings <neigh_modify>` of *every = 1* and
|
||||||
*delay = 0* are **required**. This may be combined with either
|
*delay = 0* are **required**. This may be combined with either
|
||||||
*check = no* (always update the neighbor list) or *check = yes* (only
|
*check = no* (always update the neighbor list) or *check = yes* (only
|
||||||
update the neighbor list if at least one atom has moved more than
|
update the neighbor list if at least one atom has moved more than
|
||||||
half the `neighbor list skin <neighbor>` distance since the last
|
half the :doc:`neighbor list skin <neighbor>` distance since the last
|
||||||
reneighboring). Using *check = yes* is recommended since it avoids
|
reneighboring). Using *check = yes* is recommended since it avoids
|
||||||
unneeded reneighboring steps when the system is closer to the minimum
|
unneeded reneighboring steps when the system is closer to the minimum
|
||||||
and thus atoms move only small distances. Using *check = no* may
|
and thus atoms move only small distances. Using *check = no* may be
|
||||||
be required for debugging or when coupling LAMMPS with external
|
required for debugging or when coupling LAMMPS with external codes
|
||||||
codes that require a predictable sequence of neighbor list updates.
|
that require a predictable sequence of neighbor list updates.
|
||||||
|
|
||||||
If the settings are **not** *every = 1* and *delay = 0*, LAMMPS
|
If the settings are **not** *every = 1* and *delay = 0*, LAMMPS will
|
||||||
will temporarily apply a `neigh_modify every 1 delay 0 check yes
|
temporarily apply a :doc:`neigh_modify every 1 delay 0 check yes
|
||||||
<neigh_modify>` setting during the minimization and restore the
|
<neigh_modify>` setting during the minimization and restore the
|
||||||
original setting at the end of the minimization. A corresponding
|
original setting at the end of the minimization. A corresponding
|
||||||
message will be printed to the screen and log file, if this happens.
|
message will be printed to the screen and log file, if this happens.
|
||||||
|
|||||||
@ -121,6 +121,11 @@ molecule (header keyword = inertia).
|
|||||||
ensure space is allocated for storing topology info for molecules that
|
ensure space is allocated for storing topology info for molecules that
|
||||||
are added later.
|
are added later.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Format of a molecule file
|
||||||
|
"""""""""""""""""""""""""
|
||||||
|
|
||||||
The format of an individual molecule file is similar but
|
The format of an individual molecule file is similar but
|
||||||
(not identical) to the data file read by the :doc:`read_data <read_data>`
|
(not identical) to the data file read by the :doc:`read_data <read_data>`
|
||||||
commands, and is as follows.
|
commands, and is as follows.
|
||||||
|
|||||||
@ -59,9 +59,21 @@ long cutoff, but other type pairs have a much shorter cutoff. The
|
|||||||
sized particles, where "size" may mean the physical size of the particle
|
sized particles, where "size" may mean the physical size of the particle
|
||||||
or its cutoff distance for interacting with other particles. Different
|
or its cutoff distance for interacting with other particles. Different
|
||||||
sets of bins are then used to construct the neighbor lists as as further
|
sets of bins are then used to construct the neighbor lists as as further
|
||||||
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
|
described by Shire, Hanley, and Stratford :ref:`(Shire) <multi-Shire>`
|
||||||
This imposes some extra setup overhead, but the searches themselves may
|
and Monti et al. :ref:`(Monti) <multi-Monti>`. This imposes some extra
|
||||||
be much faster. By default, each atom type defines a separate collection
|
setup overhead, but the searches themselves may be much faster.
|
||||||
|
|
||||||
|
For instance in a dense binary system in d-dimensions with a ratio of the size
|
||||||
|
of the largest to smallest collection bin :math:`\lambda`, the computational
|
||||||
|
costs of building a default neighbor list grows as :math:`\lambda^{2d}` while
|
||||||
|
the costs for *multi* grows as :math:`\lambda^d`, equivalent to the cost
|
||||||
|
of force evaluations, as argued in Monti et al. :ref:`(Monti) <multi-Monti>`.
|
||||||
|
In other words, the neighboring costs of *multi* are expected to scale the
|
||||||
|
same as force calculations, such that its relative cost is independent of
|
||||||
|
the particle size ratio. This is not the case for the default style which
|
||||||
|
becomes substantially more expensive with increasing size ratios.
|
||||||
|
|
||||||
|
By default in *multi*, each atom type defines a separate collection
|
||||||
of particles. For systems where two or more atom types have the same
|
of particles. For systems where two or more atom types have the same
|
||||||
size (either physical size or cutoff distance), the definition of
|
size (either physical size or cutoff distance), the definition of
|
||||||
collections can be customized, which can result in less overhead and
|
collections can be customized, which can result in less overhead and
|
||||||
@ -75,8 +87,11 @@ An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
|
|||||||
cutoff distance and multiple sets of bins are defined to search over for
|
cutoff distance and multiple sets of bins are defined to search over for
|
||||||
different atom types. This algorithm used to be the default *multi*
|
different atom types. This algorithm used to be the default *multi*
|
||||||
algorithm in LAMMPS but was found to be significantly slower than the new
|
algorithm in LAMMPS but was found to be significantly slower than the new
|
||||||
approach. For now we are keeping the old option in case there are use cases
|
approach. For the dense binary system, computational costs still grew as
|
||||||
where multi/old outperforms the new multi style.
|
:math:`\lambda^{2d}` at large enough :math:`\lambda`. This is equivalent
|
||||||
|
to the default style, albeit with a smaller prefactor. For now we are
|
||||||
|
keeping the old option in case there are use cases where multi/old
|
||||||
|
outperforms the new multi style.
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
@ -118,6 +133,10 @@ Default
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _bytype-Shire:
|
.. _multi-Shire:
|
||||||
|
|
||||||
**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020).
|
**(Shire)** Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
|
||||||
|
|
||||||
|
.. _multi-Monti:
|
||||||
|
|
||||||
|
**(Monti)** Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
|
||||||
|
|||||||
@ -319,7 +319,7 @@ CONFIG_ID, SIMD_SIZE, MEM_THREADS, SHUFFLE_AVAIL, FAST_MATH,
|
|||||||
THREADS_PER_ATOM, THREADS_PER_CHARGE, THREADS_PER_THREE, BLOCK_PAIR,
|
THREADS_PER_ATOM, THREADS_PER_CHARGE, THREADS_PER_THREE, BLOCK_PAIR,
|
||||||
BLOCK_BIO_PAIR, BLOCK_ELLIPSE, PPPM_BLOCK_1D, BLOCK_NBOR_BUILD,
|
BLOCK_BIO_PAIR, BLOCK_ELLIPSE, PPPM_BLOCK_1D, BLOCK_NBOR_BUILD,
|
||||||
BLOCK_CELL_2D, BLOCK_CELL_ID, MAX_SHARED_TYPES, MAX_BIO_SHARED_TYPES,
|
BLOCK_CELL_2D, BLOCK_CELL_ID, MAX_SHARED_TYPES, MAX_BIO_SHARED_TYPES,
|
||||||
PPPM_MAX_SPLINE.
|
PPPM_MAX_SPLINE, NBOR_PREFETCH.
|
||||||
|
|
||||||
CONFIG_ID can be 0. SHUFFLE_AVAIL in {0,1} indicates that inline-PTX
|
CONFIG_ID can be 0. SHUFFLE_AVAIL in {0,1} indicates that inline-PTX
|
||||||
(NVIDIA) or OpenCL extensions (Intel) should be used for horizontal
|
(NVIDIA) or OpenCL extensions (Intel) should be used for horizontal
|
||||||
|
|||||||
103
doc/src/pair_born_gauss.rst
Normal file
103
doc/src/pair_born_gauss.rst
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
.. index:: pair_style born/gauss
|
||||||
|
|
||||||
|
pair_style born/gauss command
|
||||||
|
=============================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
pair_style born/gauss cutoff
|
||||||
|
|
||||||
|
* born/gauss = name of the pair style
|
||||||
|
* cutoff = global cutoff (distance units)
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
pair_style born/gauss 10.0
|
||||||
|
pair_coeff 1 1 1 1 8.2464e13 12.48 0.042644277 0.44 3.56
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
.. versionadded:: 28Mar2023
|
||||||
|
|
||||||
|
Pair style *born/gauss* computes pairwise interactions from a combination of a Born-Mayer
|
||||||
|
repulsive term and a Gaussian attractive term according to :ref:`(Bomont) <Bomont>`:
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
E = A_0 \exp \left( -\alpha r \right) - A_1 \exp\left[ -\beta \left(r - r_0 \right)^2 \right]
|
||||||
|
\qquad r < r_c
|
||||||
|
|
||||||
|
:math:`r_c` is the cutoff.
|
||||||
|
|
||||||
|
The following coefficients must be defined for each pair of atoms
|
||||||
|
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||||
|
above, or in the data file or restart files read by the
|
||||||
|
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||||
|
commands:
|
||||||
|
|
||||||
|
* :math:`A_0` (energy units)
|
||||||
|
* :math:`\alpha` (1/distance units)
|
||||||
|
* :math:`A_1` (energy units)
|
||||||
|
* :math:`\beta` (1/(distance units)^2)
|
||||||
|
* :math:`r_0` (distance units)
|
||||||
|
* cutoff (distance units)
|
||||||
|
|
||||||
|
The last coefficient is optional. If not specified, the global cutoff is used.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||||
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
This pair style does not support mixing. Thus, coefficients for all I,J
|
||||||
|
pairs must be specified explicitly.
|
||||||
|
|
||||||
|
This pair style supports the :doc:`pair_modify <pair_modify>` shift
|
||||||
|
option for the energy of the pair interaction.
|
||||||
|
|
||||||
|
The :doc:`pair_modify <pair_modify>` table options are not relevant for
|
||||||
|
this pair style.
|
||||||
|
|
||||||
|
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||||
|
tail option for adding long-range tail corrections to energy and
|
||||||
|
pressure.
|
||||||
|
|
||||||
|
This pair style writes its information to :doc:`binary restart files
|
||||||
|
<restart>`, so pair_style and pair_coeff commands do not need to be
|
||||||
|
specified in an input script that reads a restart file.
|
||||||
|
|
||||||
|
This pair style can only be used via the *pair* keyword of the
|
||||||
|
:doc:`run_style respa <run_style>` command. It does not support the
|
||||||
|
*inner*, *middle*, *outer* keywords.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This pair style is only enabled if LAMMPS was built with the EXTRA-PAIR
|
||||||
|
package. See the :doc:`Build package <Build_package>` page for more
|
||||||
|
info.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style born <pair_born>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
|
|
||||||
|
--------------
|
||||||
|
|
||||||
|
.. _Bomont:
|
||||||
|
|
||||||
|
**(Bomont)** Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006)
|
||||||
@ -116,11 +116,12 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
|
|||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
Note that unlike for other potentials, cutoffs for EAM
|
Note that unlike for other potentials, cutoffs for EAM potentials are not
|
||||||
potentials are not set in the pair_style or pair_coeff command; they
|
set in the pair_style or pair_coeff command; they are specified in the EAM
|
||||||
are specified in the EAM potential files themselves. Likewise, the
|
potential files themselves. Likewise, valid EAM potential files usually
|
||||||
EAM potential files list atomic masses; thus you do not need to use
|
contain atomic masses; thus you may not need to use the :doc:`mass <mass>`
|
||||||
the :doc:`mass <mass>` command to specify them.
|
command to specify them, unless the potential file uses a dummy value (e.g.
|
||||||
|
0.0). LAMMPS will print a warning, if this is the case.
|
||||||
|
|
||||||
There are web sites that distribute and document EAM potentials stored
|
There are web sites that distribute and document EAM potentials stored
|
||||||
in DYNAMO or other formats:
|
in DYNAMO or other formats:
|
||||||
|
|||||||
@ -103,12 +103,13 @@ Mixing, shift, table, tail correction, restart, rRESPA info
|
|||||||
|
|
||||||
For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
|
For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
|
||||||
parameters, and the cutoff distance for these pair styles can be mixed:
|
parameters, and the cutoff distance for these pair styles can be mixed:
|
||||||
A (energy units)
|
|
||||||
sqrt(1/B) (distance units, see below)
|
* A (energy units)
|
||||||
H (energy units)
|
* :math:`\sqrt{\frac{1}{B}}` (distance units, see below)
|
||||||
sigma_h (distance units)
|
* H (energy units)
|
||||||
r_mh (distance units)
|
* :math:`r_{mh}` (distance units)
|
||||||
cutoff (distance units):ul
|
* :math:`\sigma_h` (distance units)
|
||||||
|
* cutoff (distance units)
|
||||||
|
|
||||||
The default mix value is *geometric*\ .
|
The default mix value is *geometric*\ .
|
||||||
Only *arithmetic* and *geometric* mix values are supported.
|
Only *arithmetic* and *geometric* mix values are supported.
|
||||||
@ -169,7 +170,7 @@ The *gauss* and *gauss/cut* styles are part of the EXTRA-PAIR package.
|
|||||||
They are only enabled if LAMMPS is build with that package. See the
|
They are only enabled if LAMMPS is build with that package. See the
|
||||||
:doc:`Build package <Build_package>` page for more info.
|
:doc:`Build package <Build_package>` page for more info.
|
||||||
|
|
||||||
.. versionchanged:: TBD
|
.. versionchanged:: 28Mar2023
|
||||||
|
|
||||||
Prior to this version, the *gauss* pair style did not apply
|
Prior to this version, the *gauss* pair style did not apply
|
||||||
:doc:`special_bonds <special_bonds>` factors.
|
:doc:`special_bonds <special_bonds>` factors.
|
||||||
|
|||||||
@ -279,6 +279,11 @@ statistically similar results. This is because the forces they
|
|||||||
compute depend on atom velocities. See the
|
compute depend on atom velocities. See the
|
||||||
:doc:`read_restart <read_restart>` command for more details.
|
:doc:`read_restart <read_restart>` command for more details.
|
||||||
|
|
||||||
|
Accumulated values for individual contacts are saved to to restart
|
||||||
|
files but are not saved to data files. Therefore, forces may
|
||||||
|
differ significantly when a system is reloaded using A
|
||||||
|
:doc:`read_data <read_data>` command.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -37,6 +37,9 @@ Examples
|
|||||||
pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
|
pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
|
||||||
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
|
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 heat area 0.1
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
@ -223,16 +226,19 @@ for all models except *jkr*, for which it is given implicitly according
|
|||||||
to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*,
|
to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*,
|
||||||
:math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
|
:math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
|
||||||
|
|
||||||
The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`. Here, the damping coefficient specified as part of
|
The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`.
|
||||||
the normal model is interpreted as a restitution coefficient
|
Here, the damping coefficient specified as part of the normal model is interpreted
|
||||||
:math:`e`. The damping constant :math:`\eta_n` is given by:
|
as a restitution coefficient :math:`e`. The damping constant :math:`\eta_n` is
|
||||||
|
given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\eta_n = \alpha (m_{eff}k_n)^{1/2}
|
\eta_n = \alpha (m_{eff}k_n)^{1/2}
|
||||||
|
|
||||||
For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. The parameter :math:`\alpha` is related to the restitution
|
For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. This
|
||||||
coefficient *e* according to:
|
damping model is not compatible with cohesive normal models such as *JKR* or *DMT*.
|
||||||
|
The parameter :math:`\alpha` is related to the restitution coefficient *e*
|
||||||
|
according to:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
@ -631,6 +637,34 @@ attractive force. This keyword cannot be used with the JKR or DMT models.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
The optional *heat* keyword enables heat conduction. The options currently
|
||||||
|
supported are:
|
||||||
|
|
||||||
|
1. *none*
|
||||||
|
2. *area* : :math:`k_{s}`
|
||||||
|
|
||||||
|
If the *heat* keyword is not specified, the model defaults to *none*.
|
||||||
|
|
||||||
|
For *heat* *area*, the heat
|
||||||
|
:math:`Q` conducted between two particles is given by
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
Q = k_{s} a \Delta T
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
where :math:`\Delta T` is the difference in the two particles' temperature,
|
||||||
|
:math:`k_{s}` is a non-negative numeric value for the conductivity, and
|
||||||
|
:math:`a` is the area of the contact and depends on the normal force model.
|
||||||
|
|
||||||
|
Note that the option *none* must either be used in all or none of of the
|
||||||
|
*pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and
|
||||||
|
:doc:`fix property/atom <fix_property_atom>` for more information on this
|
||||||
|
option.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
The *granular* pair style can reproduce the behavior of the
|
The *granular* pair style can reproduce the behavior of the
|
||||||
*pair gran/\** styles with the appropriate settings (some very
|
*pair gran/\** styles with the appropriate settings (some very
|
||||||
minor differences can be expected due to corrections in
|
minor differences can be expected due to corrections in
|
||||||
@ -641,7 +675,7 @@ is equivalent to *pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1*\ .
|
|||||||
The second example is equivalent to
|
The second example is equivalent to
|
||||||
*pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
|
*pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
|
||||||
The third example is equivalent to
|
The third example is equivalent to
|
||||||
*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
|
*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1 limit_damping*\ .
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -733,22 +767,30 @@ These extra quantities can be accessed by the :doc:`compute pair/local <compute_
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
All the granular pair styles are part of the GRANULAR package. It is
|
This pair style is part of the GRANULAR package. It is
|
||||||
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
only enabled if LAMMPS was built with that package.
|
||||||
|
See the :doc:`Build package <Build_package>` page for more info.
|
||||||
|
|
||||||
These pair styles require that atoms store torque and angular velocity
|
This pair style requires that atoms store per-particle radius,
|
||||||
(omega) as defined by the :doc:`atom_style <atom_style>`. They also
|
torque, and angular velocity (omega) as defined by the
|
||||||
require a per-particle radius is stored. The *sphere* atom style does
|
:doc:`atom_style sphere <atom_style>`.
|
||||||
all of this.
|
|
||||||
|
|
||||||
This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost
|
This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>`
|
||||||
atoms.
|
command so that velocities are stored by ghost atoms.
|
||||||
|
|
||||||
These pair styles will not restart exactly when using the
|
This pair style will not restart exactly when using the
|
||||||
:doc:`read_restart <read_restart>` command, though they should provide
|
:doc:`read_restart <read_restart>` command, though it should provide
|
||||||
statistically similar results. This is because the forces they
|
statistically similar results. This is because the forces it
|
||||||
compute depend on atom velocities. See the
|
computes depend on atom velocities and the atom velocities have
|
||||||
:doc:`read_restart <read_restart>` command for more details.
|
been propagated half a timestep between the force computation and
|
||||||
|
when the restart is written, due to using Velocity Verlet time
|
||||||
|
integration. See the :doc:`read_restart <read_restart>` command
|
||||||
|
for more details.
|
||||||
|
|
||||||
|
Accumulated values for individual contacts are saved to restart
|
||||||
|
files but are not saved to data files. Therefore, forces may
|
||||||
|
differ significantly when a system is reloaded using the
|
||||||
|
:doc:`read_data <read_data>` command.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -91,7 +91,8 @@ contributions from sub-styles are weighted by their scale factors, which
|
|||||||
may be fractional or even negative. Furthermore the scale factors may
|
may be fractional or even negative. Furthermore the scale factors may
|
||||||
be variables that may change during a simulation. This enables
|
be variables that may change during a simulation. This enables
|
||||||
switching smoothly between two different pair styles or two different
|
switching smoothly between two different pair styles or two different
|
||||||
parameter sets during a run.
|
parameter sets during a run in a similar fashion as could be done
|
||||||
|
with :doc:`fix adapt <fix_adapt>` or :doc:`fix alchemy <fix_alchemy>`.
|
||||||
|
|
||||||
All pair styles that will be used are listed as "sub-styles" following
|
All pair styles that will be used are listed as "sub-styles" following
|
||||||
the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the
|
the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the
|
||||||
|
|||||||
@ -68,7 +68,7 @@ Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
|
|||||||
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
|
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
|
||||||
|
|
||||||
The last coefficient is optional. If not specified, the global
|
The last coefficient is optional. If not specified, the global
|
||||||
LJ cutoff specified in the pair_style command are used.
|
LJ cutoff specified in the pair_style command is used.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -103,11 +103,12 @@ portion of the pair interaction.
|
|||||||
All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
|
All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
|
||||||
not need to be specified in an input script that reads a restart file.
|
not need to be specified in an input script that reads a restart file.
|
||||||
|
|
||||||
The *lj/cut* pair styles support the use of the
|
The *lj/cut* pair styles support the use of the *inner*, *middle*, and
|
||||||
*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
|
*outer* keywords of the :doc:`run_style respa <run_style>` command,
|
||||||
partitioned by distance at different levels of the rRESPA hierarchy.
|
meaning the pairwise forces can be partitioned by distance at different
|
||||||
The other styles only support the *pair* keyword of run_style respa.
|
levels of the rRESPA hierarchy. The other styles only support the
|
||||||
See the :doc:`run_style <run_style>` command for details.
|
*pair* keyword of run_style respa. See the :doc:`run_style <run_style>`
|
||||||
|
command for details.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -299,7 +299,7 @@ Restrictions
|
|||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of
|
The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of
|
||||||
the DPD-MESO package. It is only enabled if LAMMPS was built with
|
the DPD-MESO package. They are only enabled if LAMMPS was built with
|
||||||
that package. See the :doc:`Build package <Build_package>` page for
|
that package. See the :doc:`Build package <Build_package>` page for
|
||||||
more info.
|
more info.
|
||||||
|
|
||||||
|
|||||||
@ -132,6 +132,7 @@ accelerated styles exist.
|
|||||||
* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
|
* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
|
||||||
* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
|
* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
|
||||||
* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model
|
* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model
|
||||||
|
* :doc:`born/gauss <pair_born_gauss>` - Born-Mayer / Gaussian potential
|
||||||
* :doc:`bpm/spring <pair_bpm_spring>` - repulsive harmonic force with damping
|
* :doc:`bpm/spring <pair_bpm_spring>` - repulsive harmonic force with damping
|
||||||
* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
|
* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
|
||||||
* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
|
* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
|
||||||
|
|||||||
@ -145,7 +145,7 @@ coefficients in the formulae above:
|
|||||||
* c3
|
* c3
|
||||||
* c4
|
* c4
|
||||||
* c5
|
* c5
|
||||||
* c0 (energy units, tersoff/mod/c only):ul
|
* c0 (energy units, tersoff/mod/c only)
|
||||||
|
|
||||||
The n, :math:`\eta`, :math:`\lambda_2`, B, :math:`\lambda_1`, and A parameters are only used for
|
The n, :math:`\eta`, :math:`\lambda_2`, B, :math:`\lambda_1`, and A parameters are only used for
|
||||||
two-body interactions. The :math:`\beta`, :math:`\alpha`, c1, c2, c3, c4, c5, h
|
two-body interactions. The :math:`\beta`, :math:`\alpha`, c1, c2, c3, c4, c5, h
|
||||||
|
|||||||
@ -142,10 +142,11 @@ the :doc:`atom_style ellipsoid <atom_style>` command.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
|
:doc:`pair_coeff <pair_coeff>`,
|
||||||
:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
|
:doc:`fix nve/asphere <fix_nve_asphere>`,
|
||||||
:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
|
:doc:`compute temp/asphere <compute_temp_asphere>`,
|
||||||
:doc:gayberne <pair_gayberne>`
|
:doc:`pair_style resquared <pair_resquared>`,
|
||||||
|
:doc:`pair_style gayberne <pair_gayberne>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -1477,10 +1477,12 @@ The *Triangles* section must appear after the *Atoms* section.
|
|||||||
|
|
||||||
where the keywords have these meanings:
|
where the keywords have these meanings:
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
vx,vy,vz = translational velocity of atom
|
vx,vy,vz = translational velocity of atom
|
||||||
lx,ly,lz = angular momentum of aspherical atom
|
lx,ly,lz = angular momentum of aspherical atom
|
||||||
wx,wy,wz = angular velocity of spherical atom
|
wx,wy,wz = angular velocity of spherical atom
|
||||||
ervel = electron radial velocity (0 for fixed-core):ul
|
ervel = electron radial velocity (0 for fixed-core)
|
||||||
|
|
||||||
The velocity lines can appear in any order. This section can only be
|
The velocity lines can appear in any order. This section can only be
|
||||||
used after an *Atoms* section. This is because the *Atoms* section
|
used after an *Atoms* section. This is because the *Atoms* section
|
||||||
|
|||||||
@ -78,27 +78,41 @@ processors. See the :doc:`-partition command-line switch <Run_options>`
|
|||||||
for info on how to run LAMMPS with multiple partitions.
|
for info on how to run LAMMPS with multiple partitions.
|
||||||
|
|
||||||
Specifically, this style performs all computation except the
|
Specifically, this style performs all computation except the
|
||||||
:doc:`kspace_style <kspace_style>` portion of the force field on the first
|
:doc:`kspace_style <kspace_style>` portion of the force field on the
|
||||||
partition. This include the :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`, :doc:`neighbor list building <neighbor>`,
|
first partition. This include the :doc:`pair style <pair_style>`,
|
||||||
:doc:`fixes <fix>` including time integration, and output. The
|
:doc:`bond style <bond_style>`, :doc:`neighbor list building
|
||||||
:doc:`kspace_style <kspace_style>` portion of the calculation is
|
<neighbor>`, :doc:`fixes <fix>` including time integration, and output.
|
||||||
|
The :doc:`kspace_style <kspace_style>` portion of the calculation is
|
||||||
performed on the second partition.
|
performed on the second partition.
|
||||||
|
|
||||||
This is most useful for the PPPM kspace_style when its performance on
|
This can lead to a significant speedup, if the number of processors can
|
||||||
a large number of processors degrades due to the cost of communication
|
be easily increased and the fraction of time is spent in computing
|
||||||
in its 3d FFTs. In this scenario, splitting your P total processors
|
Kspace interactions is significant, too. The two partitions may have a
|
||||||
into 2 subsets of processors, P1 in the first partition and P2 in the
|
different number of processors. This is most useful for the PPPM
|
||||||
second partition, can enable your simulation to run faster. This is
|
kspace_style when its performance on a large number of processors
|
||||||
because the long-range forces in PPPM can be calculated at the same
|
degrades due to the cost of communication in its 3d FFTs. In this
|
||||||
time as pairwise and bonded forces are being calculated, and the FFTs
|
scenario, splitting your P total processors into 2 subsets of
|
||||||
can actually speed up when running on fewer processors.
|
processors, P1 in the first partition and P2 in the second partition,
|
||||||
|
can enable your simulation to run faster. This is because the
|
||||||
|
long-range forces in PPPM can be calculated at the same time as pairwise
|
||||||
|
and bonded forces are being calculated *and* the parallel 3d FFTs can be
|
||||||
|
faster to compute when running on fewer processors. Please note that
|
||||||
|
the scenario of using fewer MPI processes to reduce communication
|
||||||
|
overhead can also be implemented through using MPI with OpenMP threads
|
||||||
|
via the INTEL, KOKKOS, or OPENMP package. This alternative option is
|
||||||
|
typically more effective in case of a fixed number of available
|
||||||
|
processors and less complex to execute.
|
||||||
|
|
||||||
To use this style, you must define 2 partitions where P1 is a multiple
|
To use the *verlet/split* style, you must define 2 partitions with the
|
||||||
of P2. Typically having P1 be 3x larger than P2 is a good choice.
|
:doc:`-partition command-line switch <Run_options>`, where partition P1
|
||||||
The 3d processor layouts in each partition must overlay in the
|
is either the same size or an integer multiple of the size of the
|
||||||
following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by
|
partition P2. Typically having P1 be 3x larger than P2 is a good
|
||||||
Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
|
choice, since the (serial) performance of LAMMPS is often best if the
|
||||||
for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
|
time spent in the ``Pair`` computation versus ``Kspace`` is a 3:1 split.
|
||||||
|
The 3d processor layouts in each partition must overlay in the following
|
||||||
|
sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by Py2 by Pz2,
|
||||||
|
then Px1 must be an integer multiple of Px2, and similarly for Py1 a
|
||||||
|
multiple of Py2, and Pz1 a multiple of Pz2.
|
||||||
|
|
||||||
Typically the best way to do this is to let the first partition choose
|
Typically the best way to do this is to let the first partition choose
|
||||||
its own optimal layout, then require the second partition's layout to
|
its own optimal layout, then require the second partition's layout to
|
||||||
@ -122,9 +136,10 @@ of 60 and 15 processors each:
|
|||||||
When you run in 2-partition mode with the *verlet/split* style, the
|
When you run in 2-partition mode with the *verlet/split* style, the
|
||||||
thermodynamic data for the entire simulation will be output to the log
|
thermodynamic data for the entire simulation will be output to the log
|
||||||
and screen file of the first partition, which are log.lammps.0 and
|
and screen file of the first partition, which are log.lammps.0 and
|
||||||
screen.0 by default; see the :doc:`-plog and -pscreen command-line switches <Run_options>` to change this. The log and screen file
|
screen.0 by default; see the :doc:`-plog and -pscreen command-line
|
||||||
for the second partition will not contain thermodynamic output beyond the
|
switches <Run_options>` to change this. The log and screen file for the
|
||||||
first timestep of the run.
|
second partition will not contain thermodynamic output beyond the first
|
||||||
|
timestep of the run.
|
||||||
|
|
||||||
See the :doc:`Accelerator packages <Speed_packages>` page for
|
See the :doc:`Accelerator packages <Speed_packages>` page for
|
||||||
performance details of the speed-up offered by the *verlet/split*
|
performance details of the speed-up offered by the *verlet/split*
|
||||||
@ -137,70 +152,73 @@ options to support this, and strategies are discussed in :doc:`Section
|
|||||||
----------
|
----------
|
||||||
|
|
||||||
The *respa* style implements the rRESPA multi-timescale integrator
|
The *respa* style implements the rRESPA multi-timescale integrator
|
||||||
:ref:`(Tuckerman) <Tuckerman3>` with N hierarchical levels, where level 1 is
|
:ref:`(Tuckerman) <Tuckerman3>` with N hierarchical levels, where level
|
||||||
the innermost loop (shortest timestep) and level N is the outermost
|
1 is the innermost loop (shortest timestep) and level N is the outermost
|
||||||
loop (largest timestep). The loop factor arguments specify what the
|
loop (largest timestep). The loop factor arguments specify what the
|
||||||
looping factor is between levels. N1 specifies the number of
|
looping factor is between levels. N1 specifies the number of iterations
|
||||||
iterations of level 1 for a single iteration of level 2, N2 is the
|
of level 1 for a single iteration of level 2, N2 is the iterations of
|
||||||
iterations of level 2 per iteration of level 3, etc. N-1 looping
|
level 2 per iteration of level 3, etc. N-1 looping parameters must be
|
||||||
parameters must be specified.
|
specified.
|
||||||
|
|
||||||
Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
|
Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, you
|
||||||
you could choose to have bond interactions computed 8x per large
|
could choose to have bond interactions computed 8x per large timestep,
|
||||||
timestep, angle interactions computed 4x, pair interactions computed
|
angle interactions computed 4x, pair interactions computed 2x, and
|
||||||
2x, and long-range interactions once per large timestep.
|
long-range interactions once per large timestep.
|
||||||
|
|
||||||
The :doc:`timestep <timestep>` command sets the large timestep for the
|
The :doc:`timestep <timestep>` command sets the large timestep for the
|
||||||
outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for
|
outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for
|
||||||
4-level rRESPA, and the outer timestep is set to 4.0 fs, then the
|
4-level rRESPA, and the outer timestep is set to 4.0 fs, then the inner
|
||||||
inner timestep would be 8x smaller or 0.5 fs. All other LAMMPS
|
timestep would be 8x smaller or 0.5 fs. All other LAMMPS commands that
|
||||||
commands that specify number of timesteps (e.g. :doc:`thermo <thermo>`
|
specify number of timesteps (e.g. :doc:`thermo <thermo>` for thermo
|
||||||
for thermo output every N steps, :doc:`neigh_modify delay/every <neigh_modify>` parameters, :doc:`dump <dump>` every N
|
output every N steps, :doc:`neigh_modify delay/every <neigh_modify>`
|
||||||
steps, etc) refer to the outermost timesteps.
|
parameters, :doc:`dump <dump>` every N steps, etc) refer to the
|
||||||
|
outermost timesteps.
|
||||||
|
|
||||||
The rRESPA keywords enable you to specify at what level of the
|
The rRESPA keywords enable you to specify at what level of the hierarchy
|
||||||
hierarchy various forces will be computed. If not specified, the
|
various forces will be computed. If not specified, the defaults are
|
||||||
defaults are that bond forces are computed at level 1 (innermost
|
that bond forces are computed at level 1 (innermost loop), angle forces
|
||||||
loop), angle forces are computed where bond forces are, dihedral
|
are computed where bond forces are, dihedral forces are computed where
|
||||||
forces are computed where angle forces are, improper forces are
|
angle forces are, improper forces are computed where dihedral forces
|
||||||
computed where dihedral forces are, pair forces are computed at the
|
are, pair forces are computed at the outermost level, and kspace forces
|
||||||
outermost level, and kspace forces are computed where pair forces are.
|
are computed where pair forces are. The inner, middle, outer forces
|
||||||
The inner, middle, outer forces have no defaults.
|
have no defaults.
|
||||||
|
|
||||||
For fixes that support it, the rRESPA level at which a given fix is
|
For fixes that support it, the rRESPA level at which a given fix is
|
||||||
active, can be selected through the :doc:`fix_modify <fix_modify>` command.
|
active, can be selected through the :doc:`fix_modify <fix_modify>`
|
||||||
|
command.
|
||||||
|
|
||||||
The *inner* and *middle* keywords take additional arguments for
|
The *inner* and *middle* keywords take additional arguments for cutoffs
|
||||||
cutoffs that are used by the pairwise force computations. If the 2
|
that are used by the pairwise force computations. If the 2 cutoffs for
|
||||||
cutoffs for *inner* are 5.0 and 6.0, this means that all pairs up to
|
*inner* are 5.0 and 6.0, this means that all pairs up to 6.0 apart are
|
||||||
6.0 apart are computed by the inner force. Those between 5.0 and 6.0
|
computed by the inner force. Those between 5.0 and 6.0 have their force
|
||||||
have their force go ramped to 0.0 so the overlap with the next regime
|
go ramped to 0.0 so the overlap with the next regime (middle or outer)
|
||||||
(middle or outer) is smooth. The next regime (middle or outer) will
|
is smooth. The next regime (middle or outer) will compute forces for
|
||||||
compute forces for all pairs from 5.0 outward, with those from 5.0 to
|
all pairs from 5.0 outward, with those from 5.0 to 6.0 having their
|
||||||
6.0 having their value ramped in an inverse manner.
|
value ramped in an inverse manner.
|
||||||
|
|
||||||
Note that you can use *inner* and *outer* without using *middle* to
|
Note that you can use *inner* and *outer* without using *middle* to
|
||||||
split the pairwise computations into two portions instead of three.
|
split the pairwise computations into two portions instead of three.
|
||||||
Unless you are using a very long pairwise cutoff, a 2-way split is
|
Unless you are using a very long pairwise cutoff, a 2-way split is often
|
||||||
often faster than a 3-way split, since it avoids too much duplicate
|
faster than a 3-way split, since it avoids too much duplicate
|
||||||
computation of pairwise interactions near the intermediate cutoffs.
|
computation of pairwise interactions near the intermediate cutoffs.
|
||||||
|
|
||||||
Also note that only a few pair potentials support the use of the
|
Also note that only a few pair potentials support the use of the *inner*
|
||||||
*inner* and *middle* and *outer* keywords. If not, only the *pair*
|
and *middle* and *outer* keywords. If not, only the *pair* keyword can
|
||||||
keyword can be used with that pair style, meaning all pairwise forces
|
be used with that pair style, meaning all pairwise forces are computed
|
||||||
are computed at the same rRESPA level. See the doc pages for
|
at the same rRESPA level. See the doc pages for individual pair styles
|
||||||
individual pair styles for details.
|
for details.
|
||||||
|
|
||||||
Another option for using pair potentials with rRESPA is with the
|
Another option for using pair potentials with rRESPA is with the
|
||||||
*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` command. In this scenario, different
|
*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid
|
||||||
|
or hybrid/overlay <pair_hybrid>` command. In this scenario, different
|
||||||
sub-styles of the hybrid pair style are evaluated at different rRESPA
|
sub-styles of the hybrid pair style are evaluated at different rRESPA
|
||||||
levels. This can be useful, for example, to set different timesteps
|
levels. This can be useful, for example, to set different timesteps for
|
||||||
for hybrid coarse-grained/all-atom models. The *hybrid* keyword
|
hybrid coarse-grained/all-atom models. The *hybrid* keyword requires as
|
||||||
requires as many level assignments as there are hybrid sub-styles,
|
many level assignments as there are hybrid sub-styles, which assigns
|
||||||
which assigns each sub-style to a rRESPA level, following their order
|
each sub-style to a rRESPA level, following their order of definition in
|
||||||
of definition in the pair_style command. Since the *hybrid* keyword
|
the pair_style command. Since the *hybrid* keyword operates on pair
|
||||||
operates on pair style computations, it is mutually exclusive with
|
style computations, it is mutually exclusive with either the *pair* or
|
||||||
either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords.
|
the *inner*\ /\ *middle*\ /\ *outer* keywords.
|
||||||
|
|
||||||
When using rRESPA (or for any MD simulation) care must be taken to
|
When using rRESPA (or for any MD simulation) care must be taken to
|
||||||
choose a timestep size(s) that ensures the Hamiltonian for the chosen
|
choose a timestep size(s) that ensures the Hamiltonian for the chosen
|
||||||
|
|||||||
@ -11,7 +11,16 @@ Syntax
|
|||||||
set style ID keyword values ...
|
set style ID keyword values ...
|
||||||
|
|
||||||
* style = *atom* or *type* or *mol* or *group* or *region*
|
* style = *atom* or *type* or *mol* or *group* or *region*
|
||||||
* ID = atom ID range or type range or mol ID range or group ID or region ID
|
* ID = depends on style
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
for style = *atom*, ID = a range of atom IDs
|
||||||
|
for style = *type*, ID = a range of numeric types or a single type label
|
||||||
|
for style = *mol*, ID = a range of molecule IDs
|
||||||
|
for style = *group*, ID = a group ID
|
||||||
|
for style = *region*, ID = a region ID
|
||||||
|
|
||||||
* one or more keyword/value pairs may be appended
|
* one or more keyword/value pairs may be appended
|
||||||
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
|
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
|
||||||
or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
|
or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
|
||||||
@ -19,7 +28,7 @@ Syntax
|
|||||||
*spin/electron* or *radius/electron* or
|
*spin/electron* or *radius/electron* or
|
||||||
*quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
|
*quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
|
||||||
*theta* or *theta/random* or *angmom* or *omega* or
|
*theta* or *theta/random* or *angmom* or *omega* or
|
||||||
*mass* or *density* or *density/disc* or
|
*mass* or *density* or *density/disc* or *temperature* or
|
||||||
*volume* or *image* or *bond* or *angle* or *dihedral* or
|
*volume* or *image* or *bond* or *angle* or *dihedral* or
|
||||||
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
|
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
|
||||||
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
|
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
|
||||||
@ -28,18 +37,18 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*type* value = atom type
|
*type* value = numeric atom type or type label
|
||||||
value can be an atom-style variable (see below)
|
value can be an atom-style variable (see below)
|
||||||
*type/fraction* values = type fraction seed
|
*type/fraction* values = type fraction seed
|
||||||
type = new atom type
|
type = numeric atom type or type label
|
||||||
fraction = approximate fraction of selected atoms to set to new atom type
|
fraction = approximate fraction of selected atoms to set to new atom type
|
||||||
seed = random # seed (positive integer)
|
seed = random # seed (positive integer)
|
||||||
*type/ratio* values = type fraction seed
|
*type/ratio* values = type fraction seed
|
||||||
type = new atom type
|
type = numeric atom type or type label
|
||||||
fraction = exact fraction of selected atoms to set to new atom type
|
fraction = exact fraction of selected atoms to set to new atom type
|
||||||
seed = random # seed (positive integer)
|
seed = random # seed (positive integer)
|
||||||
*type/subset* values = type Nsubset seed
|
*type/subset* values = type Nsubset seed
|
||||||
type = new atom type
|
type = numeric atom type or type label
|
||||||
Nsubset = exact number of selected atoms to set to new atom type
|
Nsubset = exact number of selected atoms to set to new atom type
|
||||||
seed = random # seed (positive integer)
|
seed = random # seed (positive integer)
|
||||||
*mol* value = molecule ID
|
*mol* value = molecule ID
|
||||||
@ -100,15 +109,17 @@ Syntax
|
|||||||
value can be an atom-style variable (see below)
|
value can be an atom-style variable (see below)
|
||||||
*density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
|
*density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
|
||||||
value can be an atom-style variable (see below)
|
value can be an atom-style variable (see below)
|
||||||
|
*temperature* value = temperature for finite-size particles (temperature units)
|
||||||
|
value can be an atom-style variable (see below)
|
||||||
*volume* value = particle volume for Peridynamic particle (distance\^3 units)
|
*volume* value = particle volume for Peridynamic particle (distance\^3 units)
|
||||||
value can be an atom-style variable (see below)
|
value can be an atom-style variable (see below)
|
||||||
*image* nx ny nz
|
*image* nx ny nz
|
||||||
nx,ny,nz = which periodic image of the simulation box the atom is in
|
nx,ny,nz = which periodic image of the simulation box the atom is in
|
||||||
any of nx,ny,nz can be an atom-style variable (see below)
|
any of nx,ny,nz can be an atom-style variable (see below)
|
||||||
*bond* value = bond type for all bonds between selected atoms
|
*bond* value = numeric bond type or bond type label, for all bonds between selected atoms
|
||||||
*angle* value = angle type for all angles between selected atoms
|
*angle* value = numeric angle type or angle type label, for all angles between selected atoms
|
||||||
*dihedral* value = dihedral type for all dihedrals between selected atoms
|
*dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
|
||||||
*improper* value = improper type for all impropers between selected atoms
|
*improper* value = numeric improper type or improper type label, for all impropers between selected atoms
|
||||||
*sph/e* value = energy of SPH particles (need units)
|
*sph/e* value = energy of SPH particles (need units)
|
||||||
value can be an atom-style variable (see below)
|
value can be an atom-style variable (see below)
|
||||||
*sph/cv* value = heat capacity of SPH particles (need units)
|
*sph/cv* value = heat capacity of SPH particles (need units)
|
||||||
@ -143,15 +154,19 @@ Examples
|
|||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
set group solvent type 2
|
set group solvent type 2
|
||||||
|
set group solvent type C
|
||||||
set group solvent type/fraction 2 0.5 12393
|
set group solvent type/fraction 2 0.5 12393
|
||||||
|
set group solvent type/fraction C 0.5 12393
|
||||||
set group edge bond 4
|
set group edge bond 4
|
||||||
set region half charge 0.5
|
set region half charge 0.5
|
||||||
set type 3 charge 0.5
|
set type 3 charge 0.5
|
||||||
|
set type H charge 0.5
|
||||||
set type 1*3 charge 0.5
|
set type 1*3 charge 0.5
|
||||||
set atom * charge v_atomfile
|
set atom * charge v_atomfile
|
||||||
set atom 100*200 x 0.5 y 1.0
|
set atom 100*200 x 0.5 y 1.0
|
||||||
set atom 100 vx 0.0 vy 0.0 vz -1.0
|
set atom 100 vx 0.0 vy 0.0 vz -1.0
|
||||||
set atom 1492 type 3
|
set atom 1492 type 3
|
||||||
|
set atom 1492 type H
|
||||||
set atom * i_myVal 5
|
set atom * i_myVal 5
|
||||||
set atom * d2_Sxyz[1] 6.4
|
set atom * d2_Sxyz[1] 6.4
|
||||||
|
|
||||||
@ -181,9 +196,17 @@ properties to reset and what the new values are. Some strings like
|
|||||||
This section describes how to select which atoms to change
|
This section describes how to select which atoms to change
|
||||||
the properties of, via the *style* and *ID* arguments.
|
the properties of, via the *style* and *ID* arguments.
|
||||||
|
|
||||||
The style *atom* selects all the atoms in a range of atom IDs. The
|
.. versionchanged:: 28Mar2023
|
||||||
style *type* selects all the atoms in a range of types. The style
|
|
||||||
*mol* selects all the atoms in a range of molecule IDs.
|
Support for type labels was added for selecting atoms by type
|
||||||
|
|
||||||
|
The style *atom* selects all the atoms in a range of atom IDs.
|
||||||
|
|
||||||
|
The style *type* selects all the atoms in a range of types or type
|
||||||
|
labels. The style *type* selects atoms in one of two ways. A range
|
||||||
|
of numeric atom types can be specified. Or a single atom type label
|
||||||
|
can be specified, e.g. "C". The style *mol* selects all the atoms in
|
||||||
|
a range of molecule IDs.
|
||||||
|
|
||||||
In each of the range cases, the range can be specified as a single
|
In each of the range cases, the range can be specified as a single
|
||||||
numeric value, or a wildcard asterisk can be used to specify a range
|
numeric value, or a wildcard asterisk can be used to specify a range
|
||||||
@ -235,14 +258,23 @@ from a file.
|
|||||||
such as the molecule ID, then the floating point value is truncated to
|
such as the molecule ID, then the floating point value is truncated to
|
||||||
its integer portion, e.g. a value of 2.6 would become 2.
|
its integer portion, e.g. a value of 2.6 would become 2.
|
||||||
|
|
||||||
Keyword *type* sets the atom type for all selected atoms. The
|
.. versionchanged:: 28Mar2023
|
||||||
specified value must be from 1 to ntypes, where ntypes was set by the
|
|
||||||
:doc:`create_box <create_box>` command or the *atom types* field in the
|
|
||||||
header of the data file read by the :doc:`read_data <read_data>`
|
|
||||||
command.
|
|
||||||
|
|
||||||
Keyword *type/fraction* sets the atom type for a fraction of the
|
Support for type labels was added for setting atom, bond, angle,
|
||||||
selected atoms. The actual number of atoms changed is not guaranteed
|
dihedral, and improper types
|
||||||
|
|
||||||
|
Keyword *type* sets the atom type for all selected atoms. A specified
|
||||||
|
value can be either a numeric atom type or an atom type label. When
|
||||||
|
using a numeric type, the specified value must be from 1 to ntypes,
|
||||||
|
where ntypes was set by the :doc:`create_box <create_box>` command or
|
||||||
|
the *atom types* field in the header of the data file read by the
|
||||||
|
:doc:`read_data <read_data>` command. When using a type label it must
|
||||||
|
have been defined previously. See the :doc:`Howto type labels
|
||||||
|
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||||
|
and a general discussion of how type labels can be used.
|
||||||
|
|
||||||
|
Keyword *type/fraction* sets the atom type for a fraction of the selected
|
||||||
|
atoms. The actual number of atoms changed is not guaranteed
|
||||||
to be exactly the specified fraction (0 <= *fraction* <= 1), but
|
to be exactly the specified fraction (0 <= *fraction* <= 1), but
|
||||||
should be statistically close. Random numbers are used in such a way
|
should be statistically close. Random numbers are used in such a way
|
||||||
that a particular atom is changed or not changed, regardless of how
|
that a particular atom is changed or not changed, regardless of how
|
||||||
@ -429,6 +461,12 @@ assumed to be in mass/distance\^2 units).
|
|||||||
If none of these cases are valid, then the mass is set to the density
|
If none of these cases are valid, then the mass is set to the density
|
||||||
value directly (the input density is assumed to be in mass units).
|
value directly (the input density is assumed to be in mass units).
|
||||||
|
|
||||||
|
Keyword *temperature* sets the temperature of a finite-size particle.
|
||||||
|
Currently, only the GRANULAR package supports this attribute. The
|
||||||
|
temperature must be added using an instance of
|
||||||
|
:doc:`fix property/atom <fix_property_atom>` The values for the
|
||||||
|
temperature must be positive.
|
||||||
|
|
||||||
Keyword *volume* sets the volume of all selected particles. Currently,
|
Keyword *volume* sets the volume of all selected particles. Currently,
|
||||||
only the :doc:`atom_style peri <atom_style>` command defines particles
|
only the :doc:`atom_style peri <atom_style>` command defines particles
|
||||||
with a volume attribute. Note that this command does not adjust the
|
with a volume attribute. Note that this command does not adjust the
|
||||||
@ -455,14 +493,18 @@ simulation, but may mess up analysis of the trajectories if a LAMMPS
|
|||||||
diagnostic or your own analysis relies on the image flags to unwrap a
|
diagnostic or your own analysis relies on the image flags to unwrap a
|
||||||
molecule which straddles the periodic box.
|
molecule which straddles the periodic box.
|
||||||
|
|
||||||
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type
|
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
|
||||||
(angle type, etc) of all bonds (angles, etc) of selected atoms to the
|
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
|
||||||
specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a
|
the specified value. The value can be a numeric type from 1 to
|
||||||
particular bond (angle, etc) must be selected atoms in order for the
|
nbondtypes (nangletypes, etc). Or it can be a type label (bond type
|
||||||
change to be made. The value of nbondtype (nangletypes, etc) was set by
|
label, angle type label, etc). See the :doc:`Howto type labels
|
||||||
the *bond types* (\ *angle types*, etc) field in the header of the data
|
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||||
file read by the :doc:`read_data <read_data>` command. These keywords
|
and a general discussion of how type labels can be used. All atoms in
|
||||||
do not allow use of an atom-style variable.
|
a particular bond (angle, etc) must be selected atoms in order for the
|
||||||
|
change to be made. The value of nbondtypes (nangletypes, etc) was set
|
||||||
|
by the *bond types* (\ *angle types*, etc) field in the header of the
|
||||||
|
data file read by the :doc:`read_data <read_data>` command. These
|
||||||
|
keywords do not allow use of an atom-style variable.
|
||||||
|
|
||||||
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
|
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
|
||||||
and density of smoothed particle hydrodynamics (SPH) particles. See
|
and density of smoothed particle hydrodynamics (SPH) particles. See
|
||||||
|
|||||||
@ -49,7 +49,9 @@ pkgs = []
|
|||||||
# folder, and is not called 'MAKE' is a package
|
# folder, and is not called 'MAKE' is a package
|
||||||
|
|
||||||
for d in pkgdirs:
|
for d in pkgdirs:
|
||||||
pkg = dirs.match(d).group(1)
|
match = dirs.match(d)
|
||||||
|
if not match: continue
|
||||||
|
pkg = match.group(1)
|
||||||
if not os.path.isdir(os.path.join(src_dir, pkg)): continue
|
if not os.path.isdir(os.path.join(src_dir, pkg)): continue
|
||||||
if pkg in ['DEPEND','MAKE','STUBS']: continue
|
if pkg in ['DEPEND','MAKE','STUBS']: continue
|
||||||
pkgs.append(pkg)
|
pkgs.append(pkg)
|
||||||
|
|||||||
@ -1,5 +1,6 @@
|
|||||||
Sphinx < 6.0.0
|
Sphinx < 6.0.0
|
||||||
sphinxcontrib-spelling
|
sphinxcontrib-spelling
|
||||||
|
sphinxcontrib-jquery >=3.0.0
|
||||||
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
|
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
|
||||||
sphinx_tabs
|
sphinx_tabs
|
||||||
breathe
|
breathe
|
||||||
|
|||||||
@ -47,6 +47,7 @@ extensions = [
|
|||||||
'sphinx.ext.mathjax',
|
'sphinx.ext.mathjax',
|
||||||
'sphinx.ext.imgmath',
|
'sphinx.ext.imgmath',
|
||||||
'sphinx.ext.autodoc',
|
'sphinx.ext.autodoc',
|
||||||
|
'sphinxcontrib.jquery',
|
||||||
'sphinxfortran.fortran_domain',
|
'sphinxfortran.fortran_domain',
|
||||||
'sphinx_tabs.tabs',
|
'sphinx_tabs.tabs',
|
||||||
'table_from_list',
|
'table_from_list',
|
||||||
@ -326,6 +327,7 @@ latex_elements = {
|
|||||||
% Make ToC number fields wider to accommodate sections with >= 100 subsections
|
% Make ToC number fields wider to accommodate sections with >= 100 subsections
|
||||||
% or >= 10 subsections with >= 10 subsubsections
|
% or >= 10 subsections with >= 10 subsubsections
|
||||||
\makeatletter
|
\makeatletter
|
||||||
|
\@addtoreset{chapter}{part}
|
||||||
\renewcommand*{\sphinxtableofcontentshook}{%
|
\renewcommand*{\sphinxtableofcontentshook}{%
|
||||||
\renewcommand*\l@section{\@dottedtocline{1}{1.5em}{3.1em}}
|
\renewcommand*\l@section{\@dottedtocline{1}{1.5em}{3.1em}}
|
||||||
\renewcommand*\l@subsection{\@dottedtocline{2}{4.6em}{4.5em}}
|
\renewcommand*\l@subsection{\@dottedtocline{2}{4.6em}{4.5em}}
|
||||||
|
|||||||
@ -1,5 +1,6 @@
|
|||||||
aa
|
aa
|
||||||
aat
|
aat
|
||||||
|
Abascal
|
||||||
abc
|
abc
|
||||||
abf
|
abf
|
||||||
ABI
|
ABI
|
||||||
@ -270,6 +271,7 @@ Bialke
|
|||||||
biaxial
|
biaxial
|
||||||
bicrystal
|
bicrystal
|
||||||
Biersack
|
Biersack
|
||||||
|
biga
|
||||||
bigbig
|
bigbig
|
||||||
bigint
|
bigint
|
||||||
Bij
|
Bij
|
||||||
@ -317,6 +319,7 @@ Bogaerts
|
|||||||
Bogusz
|
Bogusz
|
||||||
Bohrs
|
Bohrs
|
||||||
boltz
|
boltz
|
||||||
|
Bomont
|
||||||
BondAngle
|
BondAngle
|
||||||
BondBond
|
BondBond
|
||||||
bondchk
|
bondchk
|
||||||
@ -355,6 +358,7 @@ br
|
|||||||
Branduardi
|
Branduardi
|
||||||
Branicio
|
Branicio
|
||||||
brennan
|
brennan
|
||||||
|
Bretonnet
|
||||||
Briels
|
Briels
|
||||||
Brien
|
Brien
|
||||||
Brilliantov
|
Brilliantov
|
||||||
@ -437,6 +441,7 @@ cfile
|
|||||||
CFL
|
CFL
|
||||||
cgdna
|
cgdna
|
||||||
CGDNA
|
CGDNA
|
||||||
|
cgmap
|
||||||
cgs
|
cgs
|
||||||
cgsdk
|
cgsdk
|
||||||
CGSDK
|
CGSDK
|
||||||
@ -629,6 +634,7 @@ cutlo
|
|||||||
cutmax
|
cutmax
|
||||||
cutoffA
|
cutoffA
|
||||||
cutoffC
|
cutoffC
|
||||||
|
cutsq
|
||||||
cuu
|
cuu
|
||||||
cv
|
cv
|
||||||
Cv
|
Cv
|
||||||
@ -1370,6 +1376,7 @@ hdnnp
|
|||||||
HDNNP
|
HDNNP
|
||||||
Hearn
|
Hearn
|
||||||
heatconduction
|
heatconduction
|
||||||
|
heatflow
|
||||||
Hebbeker
|
Hebbeker
|
||||||
Hebenstreit
|
Hebenstreit
|
||||||
Hecht
|
Hecht
|
||||||
@ -1442,6 +1449,7 @@ hux
|
|||||||
hwloc
|
hwloc
|
||||||
hx
|
hx
|
||||||
hy
|
hy
|
||||||
|
hydronium
|
||||||
hydrophobicity
|
hydrophobicity
|
||||||
hydrostatic
|
hydrostatic
|
||||||
hydrostatically
|
hydrostatically
|
||||||
@ -1791,6 +1799,7 @@ lammps
|
|||||||
Lammps
|
Lammps
|
||||||
LAMMPS
|
LAMMPS
|
||||||
lammpsbin
|
lammpsbin
|
||||||
|
lammpsdata
|
||||||
lammpsplot
|
lammpsplot
|
||||||
lammpsplugin
|
lammpsplugin
|
||||||
Lamoureux
|
Lamoureux
|
||||||
@ -1974,6 +1983,7 @@ machdyn
|
|||||||
MACHDYN
|
MACHDYN
|
||||||
Mackay
|
Mackay
|
||||||
Mackrodt
|
Mackrodt
|
||||||
|
MacLaurin
|
||||||
macOS
|
macOS
|
||||||
Macromolecules
|
Macromolecules
|
||||||
macroparticle
|
macroparticle
|
||||||
@ -1985,6 +1995,7 @@ magelec
|
|||||||
Maginn
|
Maginn
|
||||||
magneton
|
magneton
|
||||||
magnetons
|
magnetons
|
||||||
|
Mahoney
|
||||||
mainboard
|
mainboard
|
||||||
mainboards
|
mainboards
|
||||||
makefile
|
makefile
|
||||||
@ -2070,6 +2081,7 @@ mdi
|
|||||||
MDI
|
MDI
|
||||||
mdpd
|
mdpd
|
||||||
mDPD
|
mDPD
|
||||||
|
mdtraj
|
||||||
meam
|
meam
|
||||||
MEAM
|
MEAM
|
||||||
meamf
|
meamf
|
||||||
@ -2206,6 +2218,7 @@ monopole
|
|||||||
monovalent
|
monovalent
|
||||||
Montalenti
|
Montalenti
|
||||||
Montero
|
Montero
|
||||||
|
Monti
|
||||||
Mora
|
Mora
|
||||||
Morefoo
|
Morefoo
|
||||||
Morfill
|
Morfill
|
||||||
@ -2463,6 +2476,7 @@ nodeless
|
|||||||
nodeset
|
nodeset
|
||||||
nodesets
|
nodesets
|
||||||
Noehring
|
Noehring
|
||||||
|
nofix
|
||||||
Noffset
|
Noffset
|
||||||
noforce
|
noforce
|
||||||
noguess
|
noguess
|
||||||
@ -2566,7 +2580,7 @@ nvidia
|
|||||||
nvk
|
nvk
|
||||||
nvt
|
nvt
|
||||||
Nwait
|
Nwait
|
||||||
nwchem
|
NWChem
|
||||||
nx
|
nx
|
||||||
Nx
|
Nx
|
||||||
nxlo
|
nxlo
|
||||||
@ -2900,6 +2914,7 @@ PyLammps
|
|||||||
pymbar
|
pymbar
|
||||||
pymodule
|
pymodule
|
||||||
pymol
|
pymol
|
||||||
|
PySCF
|
||||||
pythonic
|
pythonic
|
||||||
pytorch
|
pytorch
|
||||||
pyy
|
pyy
|
||||||
@ -3186,6 +3201,7 @@ Sandia
|
|||||||
sandybrown
|
sandybrown
|
||||||
sanitizer
|
sanitizer
|
||||||
Sanyal
|
Sanyal
|
||||||
|
Sanz
|
||||||
Sarath
|
Sarath
|
||||||
sc
|
sc
|
||||||
scafacos
|
scafacos
|
||||||
@ -3243,6 +3259,7 @@ Sep
|
|||||||
seqdep
|
seqdep
|
||||||
Serpico
|
Serpico
|
||||||
setfl
|
setfl
|
||||||
|
setflag
|
||||||
setforce
|
setforce
|
||||||
Sethna
|
Sethna
|
||||||
setmask
|
setmask
|
||||||
@ -3478,6 +3495,7 @@ Sx
|
|||||||
sy
|
sy
|
||||||
Sy
|
Sy
|
||||||
symplectic
|
symplectic
|
||||||
|
symmetrize
|
||||||
Synechococcus
|
Synechococcus
|
||||||
sys
|
sys
|
||||||
sysdim
|
sysdim
|
||||||
@ -3487,6 +3505,7 @@ sz
|
|||||||
Sz
|
Sz
|
||||||
Tabbernor
|
Tabbernor
|
||||||
tabinner
|
tabinner
|
||||||
|
tabstyle
|
||||||
Tadmor
|
Tadmor
|
||||||
Tafipolsky
|
Tafipolsky
|
||||||
tagID
|
tagID
|
||||||
|
|||||||
1
examples/PACKAGES/alchemy/AlCu.eam.alloy
Symbolic link
1
examples/PACKAGES/alchemy/AlCu.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../potentials/AlCu.eam.alloy
|
||||||
62
examples/PACKAGES/alchemy/h2o.mol
Normal file
62
examples/PACKAGES/alchemy/h2o.mol
Normal file
@ -0,0 +1,62 @@
|
|||||||
|
# Water molecule. SPC/E model.
|
||||||
|
|
||||||
|
3 atoms
|
||||||
|
2 bonds
|
||||||
|
1 angles
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 1.12456 0.09298 1.27452
|
||||||
|
2 1.53683 0.75606 1.89928
|
||||||
|
3 0.49482 0.56390 0.65678
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1
|
||||||
|
2 2
|
||||||
|
3 2
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 -0.8472
|
||||||
|
2 0.4236
|
||||||
|
3 0.4236
|
||||||
|
|
||||||
|
Bonds
|
||||||
|
|
||||||
|
1 1 1 2
|
||||||
|
2 1 1 3
|
||||||
|
|
||||||
|
Angles
|
||||||
|
|
||||||
|
1 1 2 1 3
|
||||||
|
|
||||||
|
Shake Flags
|
||||||
|
|
||||||
|
1 1
|
||||||
|
2 1
|
||||||
|
3 1
|
||||||
|
|
||||||
|
Shake Atoms
|
||||||
|
|
||||||
|
1 1 2 3
|
||||||
|
2 1 2 3
|
||||||
|
3 1 2 3
|
||||||
|
|
||||||
|
Shake Bond Types
|
||||||
|
|
||||||
|
1 1 1 1
|
||||||
|
2 1 1 1
|
||||||
|
3 1 1 1
|
||||||
|
|
||||||
|
Special Bond Counts
|
||||||
|
|
||||||
|
1 2 0 0
|
||||||
|
2 1 1 0
|
||||||
|
3 1 1 0
|
||||||
|
|
||||||
|
Special Bonds
|
||||||
|
|
||||||
|
1 2 3
|
||||||
|
2 1 3
|
||||||
|
3 1 2
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user