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Updating to develop

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This commit is contained in:
Joel Thomas Clemmer
2022-02-18 13:58:38 -07:00
parent 5a95b35fb3 01bbb28418
commit 642b1e25f6
1971 changed files with 24552 additions and 15789 deletions
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17
.github/workflows/compile-msvc.yml vendored
View File

@ -1,5 +1,5 @@
# GitHub action to build LAMMPS on Windows with Visual C++
name: "Native Windows Compilation"
name: "Native Windows Compilation and Unit Tests"
on:
push:
@ -17,13 +17,21 @@ jobs:
with:
fetch-depth: 2
- name: Select Python version
uses: actions/setup-python@v2
with:
python-version: '3.10'
- name: Building LAMMPS via CMake
shell: bash
run: |
python3 -m pip install numpy
cmake -C cmake/presets/windows.cmake \
-D PKG_PYTHON=on \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on
-D LAMMPS_EXCEPTIONS=on \
-D ENABLE_TESTING=on
cmake --build build --config Release
- name: Run LAMMPS executable
@ -31,3 +39,8 @@ jobs:
run: |
./build/Release/lmp.exe -h
./build/Release/lmp.exe -in bench/in.lj
- name: Run Unit Tests
working-directory: build
shell: bash
run: ctest -V -C Release

46
cmake/CMakeLists.txt
View File

@ -19,6 +19,9 @@ set(SOVERSION 0)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
# collect all executables and shared libs in the top level build folder
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
set(LAMMPS_SOURCE_DIR ${LAMMPS_DIR}/src)
set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
@ -281,35 +284,19 @@ if(BUILD_MPI)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
find_package(MPI REQUIRED)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
endif()
endif()
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
if(BUILD_SHARED_LIBS)
target_link_libraries(lammps PRIVATE mpi_stubs)
if(MSVC)
target_link_libraries(lmp PRIVATE mpi_stubs)
target_include_directories(lmp INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lmp INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
endif()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
else()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
add_library(MPI::MPI_CXX ALIAS mpi_stubs)
target_sources(lammps PRIVATE ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
add_library(mpi_stubs INTERFACE)
target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
@ -373,11 +360,13 @@ if(BUILD_OMP)
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)
set(LAMMPS_OMP_COMPAT_LEVEL 4)
else()
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=3)
set(LAMMPS_OMP_COMPAT_LEVEL 3)
endif()
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
@ -591,11 +580,10 @@ if(PKG_ATC)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
if(BUILD_MPI)
target_link_libraries(atc PRIVATE MPI::MPI_CXX)
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
else()
target_link_libraries(atc PRIVATE mpi_stubs)
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} mpi_stubs)
endif()
target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
@ -691,6 +679,7 @@ endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
set_target_properties(lammps PROPERTIES PREFIX "lib")
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
@ -710,6 +699,9 @@ foreach(_DEF ${LAMMPS_DEFINES})
endforeach()
if(BUILD_SHARED_LIBS)
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
if(NOT BUILD_MPI)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
@ -749,7 +741,7 @@ install(
if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})

103
cmake/CMakeSettings.json
View File

@ -6,7 +6,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
@ -25,6 +25,54 @@
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Release-MSVC",
"generator": "Ninja",
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
}
]
},
@ -34,11 +82,16 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
@ -48,6 +101,16 @@
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
}
]
},
@ -57,7 +120,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx -DBUILD_MPI=off",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
@ -76,6 +139,21 @@
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
}
]
},
@ -85,7 +163,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=off -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort -DBUILD_MPI=off",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
@ -104,8 +182,23 @@
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
}
]
}
]
}
}

9
cmake/Modules/FindCythonize.cmake
View File

@ -8,18 +8,19 @@
#=============================================================================
if(CMAKE_VERSION VERSION_LESS 3.12)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python3 3.6 COMPONENTS Interpreter QUIET)
find_package(Python 3.6 COMPONENTS Interpreter QUIET)
endif()
# Use the Cython executable that lives next to the Python executable
# if it is a local installation.
if(Python3_EXECUTABLE)
get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
if(Python_EXECUTABLE)
get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
find_program(Cythonize_EXECUTABLE
NAMES cythonize3 cythonize cythonize.bat
HINTS ${_python_path})

51
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,50 +1,11 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)
include(ExternalProject)
ExternalProject_Add(opencl_loader
URL ${OPENCL_LOADER_URL}
URL_MD5 ${OPENCL_LOADER_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
ExternalProject_Get_Property(opencl_loader BINARY_DIR)
set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
find_package(Threads QUIET)
if(NOT WIN32)
set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
else()
set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
endif()
add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
add_dependencies(OpenCL::OpenCL opencl_loader)
set_target_properties(OpenCL::OpenCL PROPERTIES
IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
include(ExternalCMakeProject)
ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
add_library(OpenCL::OpenCL ALIAS OpenCL)

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

@ -1,10 +1,11 @@
find_package(ZLIB REQUIRED)
target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
find_package(PkgConfig REQUIRED)
pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
if(Zstd_FOUND)
find_package(PkgConfig QUIET)
if(PkgConfig_FOUND)
pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
if(Zstd_FOUND)
target_compile_definitions(lammps PRIVATE -DLAMMPS_ZSTD)
target_link_libraries(lammps PRIVATE PkgConfig::Zstd)
endif()
endif()

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

@ -422,13 +422,12 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
if(NOT BUILD_MPI)
# mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
target_link_libraries(gpu PRIVATE mpi_stubs)
else()
if(BUILD_MPI)
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
else()
target_link_libraries(gpu PRIVATE mpi_stubs)
endif()
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
target_sources(lammps PRIVATE ${GPU_SOURCES})

46
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -11,8 +11,14 @@ if(Kokkos_ENABLE_CUDA)
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
if(Kokkos_ENABLE_OPENMP AND NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
########################################################################
@ -27,6 +33,8 @@ if(DOWNLOAD_KOKKOS)
endforeach()
message(STATUS "KOKKOS download requested - we will build our own")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
# build KOKKOS downloaded libraries as static libraries but with PIC, if needed
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DBUILD_SHARED_LIBS=OFF")
if(CMAKE_REQUEST_PIC)
list(APPEND KOKKOS_LIB_BUILD_ARGS ${CMAKE_REQUEST_PIC})
endif()
@ -47,18 +55,22 @@ if(DOWNLOAD_KOKKOS)
URL ${KOKKOS_URL}
URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
)
ExternalProject_get_property(kokkos_build INSTALL_DIR)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
add_library(LAMMPS::KOKKOS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::KOKKOS PROPERTIES
add_library(LAMMPS::KOKKOSCORE UNKNOWN IMPORTED)
add_library(LAMMPS::KOKKOSCONTAINERS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::KOKKOSCORE PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscore.a"
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
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::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.5.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
@ -66,8 +78,17 @@ elseif(EXTERNAL_KOKKOS)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
# build KOKKOS internal libraries as static libraries but with PIC, if needed
if(BUILD_SHARED_LIBS)
set(BUILD_SHARED_LIBS_WAS_ON YES)
set(BUILD_SHARED_LIBS OFF)
endif()
if(CMAKE_REQUEST_PIC)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
@ -75,6 +96,9 @@ else()
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE kokkos)
target_link_libraries(lmp PRIVATE kokkos)
if(BUILD_SHARED_LIBS_WAS_ON)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_KOKKOS>)
@ -109,6 +133,12 @@ if(PKG_KSPACE)
endif()
endif()
if(PKG_PHONON)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/third_order_kokkos.cpp)
endif()
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
# detects styles which have KOKKOS version

6
cmake/Modules/Packages/ML-HDNNP.cmake
View File

@ -46,12 +46,10 @@ if(DOWNLOAD_N2P2)
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
endif()
@ -64,8 +62,8 @@ if(DOWNLOAD_N2P2)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
"PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
"PROJECT_AR=${N2P2_AR}")
"PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${CMAKE_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
"PROJECT_AR=${N2P2_AR}" "APP_CORE=nnp-convert" "APP_TRAIN=nnp-train" "APP=nnp-convert")
# echo final flag for debugging
message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")

2
cmake/Modules/Packages/PYTHON.cmake
View File

@ -3,7 +3,7 @@ if(CMAKE_VERSION VERSION_LESS 3.12)
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
find_package(Python REQUIRED COMPONENTS Development)
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

8
cmake/Modules/generate_lmpgitversion.cmake
View File

@ -24,10 +24,10 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
set(temp "${temp}bool LAMMPS_NS::LAMMPS::has_git_info() { return ${temp_git_info}; }\n")
set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_commit() { return \"${temp_git_commit}\"; }\n")
set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_branch() { return \"${temp_git_branch}\"; }\n")
set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${temp_git_describe}\"; }\n")
set(temp "${temp}#endif\n\n")
message(STATUS "Generating lmpgitversion.h...")

7
cmake/iwyu/iwyu-extra-map.imp
View File

@ -20,9 +20,14 @@
{ include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
{ include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
{ include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
{ include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
{ include: [ "@\"nstencil_.*.h\"", public, "\"style_nstencil.h\"", public ] },
{ include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
{ include: [ "\"fmt/core.h\"", private, "\"fmt/format.h\"", public ] },
{ include: [ "<float.h>", public, "<cfloat>", public ] },
{ include: [ "\"float.h\"", public, "<cfloat>", public ] },
{ include: [ "<limits.h>", public, "<climits>", public ] },
{ include: [ "\"limits.h\"", public, "<climits>", public ] },
{ include: [ "<stdio.h>", public, "<cstdio>", public ] },
{ include: [ "<bits/types/struct_rusage.h>", private, "<sys/types.h>", public ] },
{ include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
]

6
cmake/presets/gcc.cmake
View File

@ -3,19 +3,19 @@
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Og -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "g++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(MPI_C "gcc" CACHE STRING "" FORCE)
set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Og -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "1" "7 January 2022" "2022-1-7"
.TH LAMMPS "1" "17 February 2022" "2022-2-17"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

4
doc/src/Commands_all.rst
View File

@ -47,7 +47,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`dynamical_matrix (k) <dynamical_matrix>`
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
@ -117,7 +117,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`thermo <thermo>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`third_order <third_order>`
* :doc:`third_order (k) <third_order>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`

1
doc/src/Commands_fix.rst
View File

@ -129,6 +129,7 @@ OPT.
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`numdiff <fix_numdiff>`
* :doc:`numdiff/virial <fix_numdiff_virial>`
* :doc:`nve (giko) <fix_nve>`
* :doc:`nve/asphere (gi) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`

3
doc/src/Commands_pair.rst
View File

@ -119,10 +119,12 @@ OPT.
* :doc:`granular <pair_granular>`
* :doc:`gw <pair_gw>`
* :doc:`gw/zbl <pair_gw>`
* :doc:`harmonic/cut (o) <pair_harmonic_cut>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
@ -240,6 +242,7 @@ OPT.
* :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`saip/metal <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smd/hertz <pair_smd_hertz>`
* :doc:`smd/tlsph <pair_smd_tlsph>`

1
doc/src/Developer.rst
View File

@ -11,6 +11,7 @@ of time and requests from the LAMMPS user community.
:maxdepth: 1
Developer_org
Developer_cxx_vs_c_style
Developer_parallel
Developer_flow
Developer_write

384
doc/src/Developer_cxx_vs_c_style.rst Normal file
View File

@ -0,0 +1,384 @@
Code design
-----------
This section discusses some of the code design choices in LAMMPS and
overall strategy in order to assist developers to write new code that
will fit well with the remaining code. Please see the section on
:doc:`Requirements for contributed code <Modify_style>` for more
specific recommendations and guidelines. While that section is
organized more in the form of a checklist for code contributors, the
focus here is on overall code design strategy, choices made between
possible alternatives, and to discuss of some relevant C++ programming
language constructs.
Historically, the basic design philosophy of the LAMMPS C++ code was
that of a "C with classes" style. The was motivated by the desire to
make it easier to modify LAMMPS for people without significant training
in C++ programming and by trying to use data structures and code constructs
that somewhat resemble the previous implementation(s) in Fortran.
A contributing factor for this choice also was that at the time the
implementation of C++ compilers was not always very mature and some of
the advanced features contained bugs or were not functioning exactly
as the standard required; plus there was some disagreement between
compiler vendors about how to interpret the C++ standard documents.
However, C++ compilers have advanced a lot since then and with the
transition to requiring the C++11 standard in 2020 as the minimum C++ language
standard for LAMMPS, the decision was made to also replace some of the
C-style constructs with equivalent C++ functionality, either from the
C++ standard library or as custom classes or function, in order to
improve readability of the code and to increase code reuse through
abstraction of commonly used functionality.
.. note::
Please note that as of spring 2022 there is still a sizable chunk of
legacy code in LAMMPS that has not yet been refactored to reflect these
style conventions in full. LAMMPS has a large code base and many
different contributors and there also is a hierarchy of precedence
in which the code is adapted. Highest priority has the code in the
``src`` folder, followed by code in packages in order of their popularity
and complexity (simpler code is adapted sooner), followed by code
in the ``lib`` folder. Source code that is downloaded during compilation
is not subject to the conventions discussed here.
Object oriented code
^^^^^^^^^^^^^^^^^^^^
LAMMPS is designed to be an object oriented code, that is each
simulation is represented by an instance of the LAMMPS class. When
running in parallel, of course, each MPI process will create such an
instance. This can be seen in the ``main.cpp`` file where the core
steps of running a LAMMPS simulation are the following 3 lines of code:
.. code-block:: C++
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
delete lammps;
The first line creates a LAMMPS class instance and passes the command
line arguments and the global communicator to its constructor. The
second line tells the LAMMPS instance to process the input (either from
standard input or the provided input file) until the end. And the third
line deletes that instance again. The remainder of the main.cpp file
are for error handling, MPI configuration and other special features.
In the constructor of the LAMMPS class instance the basic LAMMPS class hierarchy
is created as shown in :ref:`class-topology`. While processing the input further
class instances are created, or deleted, or replaced and specific member functions
of specific classes are called to trigger actions like creating atoms, computing
forces, computing properties, propagating the system, or writing output.
Compositing and Inheritance
===========================
LAMMPS makes extensive use of the object oriented programming (OOP)
principles of *compositing* and *inheritance*. Classes like the
``LAMMPS`` class are a **composite** containing pointers to instances of
other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
``Modify``, and so on. Each of these classes implement certain
functionality by storing and manipulating data related to the simulation
and providing member functions that trigger certain actions. Some of
those classes like ``Force`` are a composite again containing instances
of classes describing the force interactions or ``Modify`` containing
and calling fixes and computes. In most cases (e.g. ``AtomVec``, ``Comm``,
``Pair``, or ``Bond``) there is only one instance of those member classes
allowed, but in a few cases (e.g. ``Region``, ``Fix``, ``Compute``, or
``Dump``) there can be multiple instances and the parent class is
maintaining a list of the pointers of instantiated classes instead
of a single pointer.
Changing behavior or adjusting how LAMMPS handles a simulation is
implemented via **inheritance** where different variants of the
functionality are realized by creating *derived* classes that can share
common functionality in their base class and provide a consistent
interface where the derived classes replace (dummy or pure) functions in
the base class. The higher level classes can then call those methods of
the instantiated classes without having to know which specific derived
class variant was instantiated. In the LAMMPS documentation those
derived classes are usually referred to a "styles", e.g. pair styles,
fix styles, atom styles and so on.
This is the origin of the flexibility of LAMMPS and facilitates for
example to compute forces for very different non-bonded potential
functions by having different pair styles (implemented as different
classes derived from the ``Pair`` class) where the evaluation of the
potential function is confined to the implementation of the individual
classes. Whenever a new :doc:`pair_style` or :doc:`bond_style` or
:doc:`comm_style` or similar command is processed in the LAMMPS input
any existing class instance is deleted and a new instance created in
it place.
Classes derived from ``Fix`` or ``Compute`` represent a different facet
of LAMMPS' flexibility as there can be multiple instances of them an
their member functions will be called at different phases of the time
integration process (as explained in `Developer_flow`). This way
multiple manipulations of the entire or parts of the system can be
programmed (with fix styles) or different computations can be performed
and accessed and further processed or output through a common interface
(with compute styles).
Further code sharing is possible by creating derived classes from the
derived classes (for instance to implement an accelerated version of a
pair style) where then only a subset of the methods are replaced with
the accelerated versions.
Polymorphism
============
Polymorphism and dynamic dispatch are another OOP feature that play an
important part of how LAMMPS selects which code to execute. In a nutshell,
this is a mechanism where the decision of which member function to call
from a class is determined at runtime and not when the code is compiled.
To enable it, the function has to be declared as ``virtual`` and all
corresponding functions in derived classes should be using the ``override``
property. Below is a brief example.
.. code-block:: c++
class Base {
public:
virtual ~Base() = default;
void call();
void normal();
virtual void poly();
};
void Base::call() {
normal();
poly();
}
class Derived : public Base {
public:
~Derived() override = default;
void normal();
void poly() override;
};
// [....]
Base *base1 = new Base();
Base *base2 = new Derived();
base1->call();
base2->call();
The difference in behavior of the ``normal()`` and the ``poly()`` member
functions is in which of the two member functions is called when
executing `base1->call()` and `base2->call()`. Without polymorphism, a
function within the base class will call only member functions within
the same scope, that is ``Base::call()`` will always call
``Base::normal()``. But for the `base2->call()` the call for the
virtual member function will be dispatched to ``Derived::poly()``
instead. This mechanism allows to always call functions within the
scope of the class type that was used to create the class instance, even
if they are assigned to a pointer using the type of a base class. This
is the desired behavior, and thanks to dynamic dispatch, LAMMPS can even
use styles that are loaded at runtime from a shared object file with the
:doc:`plugin command <plugin>`.
A special case of virtual functions are so-called pure functions. These
are virtual functions that are initialized to 0 in the class declaration
(see example below).
.. code-block:: c++
class Base {
public:
virtual void pure() = 0;
};
This has the effect that it will no longer be possible to create an
instance of the base class and that derived classes **must** implement
these functions. Many of the functions listed with the various class
styles in the section :doc:`Modify` are such pure functions. The
motivation for this is to define the interface or API of the functions
but defer the implementation to the derived classes.
However, there are downsides to this. For example, calls to virtual
functions from within a constructor, will not be in the scope of the
derived class and thus it is good practice to either avoid calling them
or to provide an explicit scope like in ``Base::poly()``. Furthermore,
any destructors in classes containing virtual functions should be
declared virtual, too, so they are processed in the expected order
before types are removed from dynamic dispatch.
.. admonition:: Important Notes
In order to be able to detect incompatibilities and to avoid unexpected
behavior already at compile time, it is crucial that all member functions
that are intended to replace a virtual or pure function use the ``override``
property keyword. For the same reason it should be avoided to use overloads
or default arguments for virtual functions as they lead to confusion over
which function is supposed to override which and which arguments need to be
declared.
Style Factories
===============
In order to create class instances of the different styles, LAMMPS often
uses a programming pattern called `Factory`. Those are functions that create
an instance of a specific derived class, say ``PairLJCut`` and return a pointer
to the type of the common base class of that style, ``Pair`` in this case.
To associate the factory function with the style keyword, an ``std::map``
class is used in which function pointers are indexed by their keyword
(for example "lj/cut" for ``PairLJCut`` and "morse" ``PairMorse``).
A couple of typedefs help to keep the code readable and a template function
is used to implement the actual factory functions for the individual classes.
I/O and output formatting
^^^^^^^^^^^^^^^^^^^^^^^^^
C-style stdio versus C++ style iostreams
========================================
LAMMPS chooses to use the "stdio" library of the standard C library for
reading from and writing to files and console instead of C++
"iostreams". This is mainly motivated by the better performance, better
control over formatting, and less effort to achieve specific formatting.
Since mixing "stdio" and "iostreams" can lead to unexpected behavior using
the latter is strongly discouraged. Also output to the screen should not
use the predefined ``stdout`` FILE pointer, but rather the ``screen`` and
``logfile`` FILE pointers managed by the LAMMPS class. Furthermore, output
should only be done by MPI rank 0 (``comm->me == 0``) and output that is
send to both ``screen`` and ``logfile`` should use the
:cpp:func:`utils::logmesg() convenience function <LAMMPS_NS::utils::logmesg>`.
We also discourage the use for stringstreams as the bundled {fmt} library
and the customized tokenizer classes can provide the same functionality
in a cleaner way with better performance. This will also help to retain
a consistent programming style despite the many different contributors.
Formatting with the {fmt} library
===================================
The LAMMPS source code includes a copy of the `{fmt} library
<https://fmt.dev>`_ which is preferred over formatting with the
"printf()" family of functions. The primary reason is that it allows a
typesafe default format for any type of supported data. This is
particularly useful for formatting integers of a given size (32-bit or
64-bit) which may require different format strings depending on compile
time settings or compilers/operating systems. Furthermore, {fmt} gives
better performance, has more functionality, a familiar formatting syntax
that has similarities to ``format()`` in Python, and provides a facility
that can be used to integrate format strings and a variable number of
arguments into custom functions in a much simpler way that the varargs
mechanism of the C library. Finally, {fmt} has been included into the
C++20 language standard, so changes to adopt it are future proof.
Formatted strings are frequently created by calling the
``fmt::format()`` function which will return a string as ``std::string``
class instance. In contrast to the ``%`` placeholder in ``printf()``,
the {fmt} library uses ``{}`` to embed format descriptors. In the
simplest case, no additional characters are needed as {fmt} will choose
the default format based on the data type of the argument. Alternatively
The ``fmt::print()`` function may be used instead of ``printf()`` or
``fprintf()``. In addition, several LAMMPS output functions, that
originally accepted a single string as arguments have been overloaded to
accept a format string with optional arguments as well (e.g.
``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
Summary of the {fmt} format syntax
==================================
The syntax of the format string is "{[<argument id>][:<format spec>]}",
where either the argument id or the format spec (separated by a colon
':') is optional. The argument id is usually a number starting from 0
that is the index to the arguments following the format string. By
default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.). The most
common case for using argument id would be to use the same argument in
multiple places in the format string without having to provide it as an
argument multiple times. In LAMMPS the argument id is rarely used.
More common is the use of the format specifier, which starts with a
colon. This may optionally be followed by a fill character (default is
' '). If provided, the fill character **must** be followed by an
alignment character ('<', '^', '>' for left, centered, or right
alignment (default)). The alignment character may be used without a fill
character. The next important format parameter would be the minimum
width, which may be followed by a dot '.' and a precision for floating
point numbers. The final character in the format string would be an
indicator for the "presentation", i.e. 'd' for decimal presentation of
integers, 'x' for hexadecimal, 'o' for octal, 'c' for character
etc. This mostly follows the "printf()" scheme but without requiring an
additional length parameter to distinguish between different integer
widths. The {fmt} library will detect those and adapt the formatting
accordingly. For floating point numbers there are correspondingly, 'g'
for generic presentation, 'e' for exponential presentation, and 'f' for
fixed point presentation.
Thus "{:8}" would represent *any* type argument using at least 8
characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
"{:>8}" as right aligned. If a specific presentation is selected, the
argument type must be compatible or else the {fmt} formatting code will
throw an exception. Some format string examples are given below:
.. code-block:: C
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
label, time_min, time, time_max, time_sq, tmp);
utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n",
xlattice,ylattice,zlattice);
which will create the following output lines:
.. parsed-literal::
CPU time: 0:02:16
Pair | 2.0133 | 2.0133 | 2.0133 | 0.0 | 84.21
4 = max # of 1-2 neighbors
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
A special feature of the {fmt} library is that format parameters like
the width or the precision may be also provided as arguments. In that
case a nested format is used where a pair of curly braces (with an
optional argument id) "{}" are used instead of the value, for example
"{:{}d}" will consume two integer arguments, the first will be the value
shown and the second the minimum width.
For more details and examples, please consult the `{fmt} syntax
documentation <https://fmt.dev/latest/syntax.html>`_ website.
Memory management
^^^^^^^^^^^^^^^^^
Dynamical allocation of data and objects should be done with either the
C++ commands "new" and "delete/delete[]" or using member functions of
the ``Memory`` class, most commonly, ``Memory::create()``,
``Memory::grow()``, and ``Memory::destroy()``. The use of ``malloc()``,
``calloc()``, ``realloc()`` and ``free()`` directly is strongly
discouraged. To simplify adapting legacy code into the LAMMPS code base
the member functions ``Memory::smalloc()``, ``Memory::srealloc()``, and
``Memory::sfree()`` are available.
Using those custom memory allocation functions is motivated by the
following considerations:
- memory allocation failures on *any* MPI rank during a parallel run
will trigger an immediate abort of the entire parallel calculation
instead of stalling it
- a failing "new" will trigger an exception which is also captured by
LAMMPS and triggers a global abort
- allocation of multi-dimensional arrays will be done in a C compatible
fashion but so that the storage of the actual data is stored in one
large consecutive block and thus when MPI communication is needed,
only this storage needs to be communicated (similar to Fortran arrays)
- the "destroy()" and "sfree()" functions may safely be called on NULL
pointers
- the "destroy()" functions will nullify the pointer variables making
"use after free" errors easy to detect
- it is possible to use a larger than default memory alignment (not on
all operating systems, since the allocated storage pointers must be
compatible with ``free()`` for technical reasons)
In the practical implementation of code this means that any pointer variables
that are class members should be initialized to a ``nullptr`` value in their
respective constructors. That way it would be safe to call ``Memory::destroy()``
or ``delete[]`` on them before *any* allocation outside the constructor.
This helps to prevent memory leaks.

55
doc/src/Developer_notes.rst
View File

@ -7,6 +7,61 @@ typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs. The topics
on this page are intended to document code functionality at a higher level.
Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
It is frequently required for a class in LAMMPS to read in additional
data from a file, most commonly potential parameters from a potential
file for manybody potentials. LAMMPS provides several custom classes
and convenience functions to simplify the process. This offers the
following benefits:
- better code reuse and fewer lines of code needed to implement reading
and parsing data from a file
- better detection of format errors, incompatible data, and better error messages
- exit with an error message instead of silently converting only part of the
text to a number or returning a 0 on unrecognized text and thus reading incorrect values
- re-entrant code through avoiding global static variables (as used by ``strtok()``)
- transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
(the text to value conversion functions **only** accept ASCII characters)
In most cases (e.g. potential files) the same data is needed on all MPI
ranks. Then it is best to do the reading and parsing only on MPI rank
0, and communicate the data later with one or more ``MPI_Bcast()``
calls. For reading generic text and potential parameter files the
custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
are available. Those classes allow to read the file as individual lines
for which they can return a tokenizer class (see below) for parsing the
line, or they can return blocks of numbers as a vector directly. The
documentation on `File reader classes <file-reader-classes>`_ contains
an example for a typical case.
When reading per-atom data, the data in the file usually needs include
an atom ID so it can be associated with a particular atom. In that case
the data can be read in multi-line chunks and broadcast to all MPI ranks
with :cpp:func:`utils::read_lines_from_file()
<LAMMPS_NS::utils::read_lines_from_file>`. Those chunks are then
split into lines, parsed, and applied only to atoms the MPI rank
"owns".
For splitting a string (incrementally) into words and optionally
converting those to numbers, the :cpp:class:`Tokenizer
<LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer
<LAMMPS_NS::ValueTokenizer>` can be used. Those provide a superset of
the functionality of ``strtok()`` from the C-library and the latter also
includes conversion to different types. Any errors while processing the
string in those classes will result in an exception, which can be caught
and the error processed as needed. Unlike the C-library functions
``atoi()``, ``atof()``, ``strtol()``, or ``strtod()`` the conversion
will check if the converted text is a valid integer of floating point
number and will not silently return an unexpected or incorrect value.
For example, ``atoi()`` will return 12 when converting "12.5" while the
ValueTokenizer class will throw an :cpp:class:`InvalidIntegerException
<LAMMPS_NS::InvalidIntegerException>` if
:cpp:func:`ValueTokenizer::next_int()
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

2
doc/src/Developer_org.rst
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@ -225,7 +225,7 @@ follows:
commands in an input script.
- The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
parent class is for non-bonded or pairwise forces, which in LAMMPS
also includes many-body forces such as the Tersoff 3-body potential if
those are computed by walking pairwise neighbor lists. The Bond,
Angle, Dihedral, Improper parent classes are styles for bonded

70
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@ -21,18 +21,21 @@ In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
but it will read in a whole line (i.e. until the end of line or end
of file), but store only as many characters as will fit into the buffer
including a final newline character and the terminating NULL byte.
If the line in the file is longer it will thus be truncated in the buffer.
This function is used by :cpp:func:`read_lines_from_file` to read individual
lines but make certain they follow the size constraints.
The :cpp:func:`utils::fgets_trunc() <LAMMPS_NS::utils::fgets_trunc>`
function will work similar for ``fgets()`` but it will read in a whole
line (i.e. until the end of line or end of file), but store only as many
characters as will fit into the buffer including a final newline
character and the terminating NULL byte. If the line in the file is
longer it will thus be truncated in the buffer. This function is used
by :cpp:func:`utils::read_lines_from_file()
<LAMMPS_NS::utils::read_lines_from_file>` to read individual lines but
make certain they follow the size constraints.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
The :cpp:func:`utils::read_lines_from_file()
<LAMMPS_NS::utils::read_lines_from_file>` function will read the
requested number of lines of a maximum length into a buffer and will
return 0 if successful or 1 if not. It also guarantees that all lines
are terminated with a newline character and the entire buffer with a
NULL character.
----------
@ -62,7 +65,7 @@ silently returning the result of a partial conversion or zero in cases
where the string is not a valid number. This behavior improves
detecting typos or issues when processing input files.
Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
Similarly the :cpp:func:`utils::logical() <LAMMPS_NS::utils::logical>` function
will convert a string into a boolean and will only accept certain words.
The *do_abort* flag should be set to ``true`` in case this function
@ -70,8 +73,8 @@ is called only on a single MPI rank, as that will then trigger the
a call to ``Error::one()`` for errors instead of ``Error::all()``
and avoids a "hanging" calculation when run in parallel.
Please also see :cpp:func:`is_integer() <LAMMPS_NS::utils::is_integer>`
and :cpp:func:`is_double() <LAMMPS_NS::utils::is_double>` for testing
Please also see :cpp:func:`utils::is_integer() <LAMMPS_NS::utils::is_integer>`
and :cpp:func:`utils::is_double() <LAMMPS_NS::utils::is_double>` for testing
strings for compliance without conversion.
----------
@ -205,6 +208,9 @@ Convenience functions
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: getsyserror
:project: progguide
@ -337,11 +343,11 @@ This code example should produce the following output:
.. doxygenclass:: LAMMPS_NS::InvalidIntegerException
:project: progguide
:members: what
:members:
.. doxygenclass:: LAMMPS_NS::InvalidFloatException
:project: progguide
:members: what
:members:
----------
@ -390,21 +396,26 @@ A typical code segment would look like this:
----------
.. file-reader-classes:
File reader classes
-------------------
The purpose of the file reader classes is to simplify the recurring task
of reading and parsing files. They can use the
:cpp:class:`LAMMPS_NS::ValueTokenizer` class to process the read in
text. The :cpp:class:`LAMMPS_NS::TextFileReader` is a more general
version while :cpp:class:`LAMMPS_NS::PotentialFileReader` is specialized
to implement the behavior expected for looking up and reading/parsing
files with potential parameters in LAMMPS. The potential file reader
class requires a LAMMPS instance, requires to be run on MPI rank 0 only,
will use the :cpp:func:`LAMMPS_NS::utils::get_potential_file_path`
function to look up and open the file, and will call the
:cpp:class:`LAMMPS_NS::Error` class in case of failures to read or to
convert numbers, so that LAMMPS will be aborted.
:cpp:class:`ValueTokenizer <LAMMPS_NS::ValueTokenizer>` class to process
the read in text. The :cpp:class:`TextFileReader
<LAMMPS_NS::TextFileReader>` is a more general version while
:cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>` is
specialized to implement the behavior expected for looking up and
reading/parsing files with potential parameters in LAMMPS. The
potential file reader class requires a LAMMPS instance, requires to be
run on MPI rank 0 only, will use the
:cpp:func:`utils::get_potential_file_path
<LAMMPS_NS::utils::get_potential_file_path>` function to look up and
open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
case of failures to read or to convert numbers, so that LAMMPS will be
aborted.
.. code-block:: C++
:caption: Use of PotentialFileReader class in pair style coul/streitz
@ -479,10 +490,10 @@ provided, as that is used to determine whether a new page of memory
must be used.
The :cpp:class:`MyPage <LAMMPS_NS::MyPage>` class offers two ways to
reserve a chunk: 1) with :cpp:func:`get() <LAMMPS_NS::MyPage::get>` the
chunk size needs to be known in advance, 2) with :cpp:func:`vget()
reserve a chunk: 1) with :cpp:func:`MyPage::get() <LAMMPS_NS::MyPage::get>` the
chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
<LAMMPS_NS::MyPage::vget>` a pointer to the next chunk is returned, but
its size is registered later with :cpp:func:`vgot()
its size is registered later with :cpp:func:`MyPage::vgot()
<LAMMPS_NS::MyPage::vgot>`.
.. code-block:: C++
@ -585,4 +596,3 @@ the communication buffers.
.. doxygenunion:: LAMMPS_NS::ubuf
:project: progguide

7
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@ -1941,6 +1941,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Compute ID for fix numdiff does not exist*
Self-explanatory.
*Compute ID for fix numdiff/virial does not exist*
Self-explanatory.
*Compute ID for fix store/state does not exist*
Self-explanatory.
@ -3796,6 +3799,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory. Efficient loop over all atoms for numerical
difference requires consecutive atom IDs.
*Fix numdiff/virial must use group all*
Virial contributions computed by this fix are
computed on all atoms.
*Fix nve/asphere requires extended particles*
This fix can only be used for particles with a shape setting.

2
doc/src/Errors_warnings.rst
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@ -416,7 +416,7 @@ This will most likely cause errors in kinetic fluctuations.
not defined for the specified atom style.
*Molecule has bond topology but no special bond settings*
This means the bonded atoms will not be excluded in pair-wise
This means the bonded atoms will not be excluded in pairwise
interactions.
*Molecule template for create_atoms has multiple molecules*

2
doc/src/Howto_pylammps.rst
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@ -545,6 +545,6 @@ Feedback and Contributing
-------------------------
If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
and ideas on how to improve it to Richard Berger (richard.berger@outlook.com). We also
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
and maybe their latest research results.

2
doc/src/Intro_authors.rst
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@ -8,7 +8,7 @@ University:
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* Axel Kohlmeyer, akohlmey at gmail.com
* Richard Berger, richard.berger at temple.edu
* Richard Berger, richard.berger at outlook.com
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: https://www.lammps.org

6
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@ -13,6 +13,7 @@ functions. They do not directly call the LAMMPS library.
- :cpp:func:`lammps_fix_external_set_virial_peratom`
- :cpp:func:`lammps_fix_external_set_vector_length`
- :cpp:func:`lammps_fix_external_set_vector`
- :cpp:func:`lammps_flush_buffers`
- :cpp:func:`lammps_free`
- :cpp:func:`lammps_is_running`
- :cpp:func:`lammps_force_timeout`
@ -72,6 +73,11 @@ where such memory buffers were allocated that require the use of
-----------------------
.. doxygenfunction:: lammps_flush_buffers
:project: progguide
-----------------------
.. doxygenfunction:: lammps_free
:project: progguide

34
doc/src/Modify_style.rst
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@ -305,6 +305,40 @@ you are uncertain, please ask.
FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
convenience function where possible.
- Usage of C++11 `virtual`, `override`, `final` keywords: Please follow the
`C++ Core Guideline C.128 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rh-override>`_.
That means, you should only use `virtual` to declare a new virtual
function, `override` to indicate you are overriding an existing virtual
function, and `final` to prevent any further overriding.
- Trivial destructors: Prefer not writing destructors when they are empty and `default`.
.. code-block:: c++
// don't write destructors for A or B like this
class A : protected Pointers {
public:
A();
~A() override {}
};
class B : protected Pointers {
public:
B();
~B() override = default;
};
// instead, let the compiler create the implicit default destructor by not writing it
class A : protected Pointers {
public:
A();
};
class B : protected Pointers {
public:
B();
};
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not** contain
any ``using`` statements. Typically that would be only the header for

4
doc/src/Run_output.rst
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@ -106,7 +106,7 @@ individual ranks. Here is an example output for this section:
----------
The third section above lists the number of owned atoms (Nlocal),
ghost atoms (Nghost), and pair-wise neighbors stored per processor.
ghost atoms (Nghost), and pairwise neighbors stored per processor.
The max and min values give the spread of these values across
processors with a 10-bin histogram showing the distribution. The total
number of histogram counts is equal to the number of processors.
@ -114,7 +114,7 @@ number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pair-wise neighbors and special neighbors that LAMMPS keeps track
for pairwise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
of times neighbor lists were rebuilt is tallied, as is the number of
potentially *dangerous* rebuilds. If atom movement triggered neighbor

2
doc/src/Speed_kokkos.rst
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@ -214,7 +214,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
The default for the :doc:`package kokkos <package>` command when
running on KNL is to use "half" neighbor lists and set the Newton flag
to "on" for both pairwise and bonded interactions. This will typically
be best for many-body potentials. For simpler pair-wise potentials, it
be best for many-body potentials. For simpler pairwise potentials, it
may be faster to use a "full" neighbor list with Newton flag to "off".
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
the default :doc:`package kokkos <package>` options. See its page for

29
doc/src/Tools.rst
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@ -277,17 +277,34 @@ at ens-lyon.fr, alain.dequidt at uca.fr
eam database tool
-----------------------------
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
Zr. The files can then be used with the :doc:`pair_style eam/alloy <pair_eam>` command.
The tools/eam_database directory contains a Fortran and a Python program
that will generate EAM alloy setfl potential files for any combination
of the 17 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg,
Co, Ti, Zr, Cr. The files can then be used with the :doc:`pair_style
eam/alloy <pair_eam>` command.
The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
and is based on his paper:
The Fortran version of the tool was authored by Xiaowang Zhou (Sandia),
xzhou at sandia.gov, with updates from Lucas Hale (NIST) lucas.hale at
nist.gov and is based on his paper:
X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
144113 (2004).
The parameters for Cr were taken from:
Lin Z B, Johnson R A and Zhigilei L V, Phys. Rev. B 77 214108 (2008).
The Python version of the tool was authored by Germain Clavier
(TU Eindhoven) g.m.g.c.clavier at tue.nl or germain.clavier at gmail.com
.. note::
The parameters in the database are only optimized for individual
elements. The mixed parameters for interactions between different
elements generated by this tool are derived from simple mixing rules
and are thus inferior to parameterizations that are specifically
optimized for specific mixtures and combinations of elements.
----------
.. _eamgn:

2
doc/src/balance.rst
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@ -383,7 +383,7 @@ multiple groups, its weight is the product of the weight factors.
This weight style is useful in combination with pair style
:doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
potential with a fast pair-wise potential. It is also useful when
potential with a fast pairwise potential. It is also useful when
using :doc:`run_style respa <run_style>` where some portions of the
system have many bonded interactions and others none. It assumes that
the computational cost for each group remains constant over time.

2
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@ -141,7 +141,7 @@ Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
:doc:`thermo_style <thermo_style>`,
:doc:`thermo_style <thermo_style>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
Default
"""""""

2
doc/src/compute_pressure_cylinder.rst
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@ -61,7 +61,7 @@ Restrictions
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pair-wise force
due to exclusions for special bonds) and requires pairwise force
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included

12
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@ -17,13 +17,14 @@ Syntax
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
.. parsed-literal::
*append* arg = *yes* or *no*
*at* arg = N
N = index of frame written upon first dump
*balance* arg = *yes* or *no*
*buffer* arg = *yes* or *no*
*delay* arg = Dstep
Dstep = delay output until this timestep
@ -668,6 +669,14 @@ keywords are set to non-default values (i.e. the number of dump file
pieces is not equal to the number of procs), then sorting cannot be
performed.
In a parallel run, the per-processor dump file pieces can have
significant imbalance in number of lines of per-atom info. The *balance*
keyword determines whether the number of lines in each processor
snapshot are balanced to be nearly the same. A balance value of *no*
means no balancing will be done, while *yes* means balancing will be
performed. This balancing preserves dump sorting order. For a serial
run, this option is ignored since the output is already balanced.
.. note::
Unless it is required by the dump style, sorting dump file
@ -833,6 +842,7 @@ Default
The option defaults are
* append = no
* balance = no
* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz*
* element = "C" for every atom type
* every = whatever it was set to via the :doc:`dump <dump>` command

9
doc/src/dynamical_matrix.rst
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@ -1,8 +1,11 @@
.. index:: dynamical_matrix
.. index:: dynamical_matrix/kk
dynamical_matrix command
========================
Accelerator Variants: dynamical_matrix/kk
Syntax
""""""
@ -56,6 +59,12 @@ If the style eskm is selected, the dynamical matrix will be in units of
inverse squared femtoseconds. These units will then conveniently leave
frequencies in THz.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

3
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@ -271,7 +271,8 @@ accelerated styles exist.
* :doc:`npt/eff <fix_nh_eff>` - NPT for nuclei and electrons in the electron force field model
* :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
* :doc:`npt/uef <fix_nh_uef>` - NPT style time integration with diagonal flow
* :doc:`numdiff <fix_numdiff>` - compute derivatives of per-atom data from finite differences
* :doc:`numdiff <fix_numdiff>` - numerically approximate atomic forces using finite energy differences
* :doc:`numdiff/virial <fix_numdiff_virial>` - numerically approximate virial stress tensor using finite energy differences
* :doc:`nve <fix_nve>` - constant NVE time integration
* :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` - NVE for aspherical particles without forces

75
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@ -20,13 +20,13 @@ Syntax
.. parsed-literal::
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *rxd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
*pH* value = pH of the solution (can be specified as an equal-style variable)
*pKa* value = acid dissociation constant
*pKb* value = base dissociation constant
*pIp* value = chemical potential of free cations
*pIm* value = chemical potential of free anions
*pKs* value = solution self-dissociation constant
*pKa* value = acid dissociation constant (in the -log10 representation)
*pKb* value = base dissociation constant (in the -log10 representation)
*pIp* value = activity (effective concentration) of free cations (in the -log10 representation)
*pIm* value = activity (effective concentration) of free anions (in the -log10 representation)
*pKs* value = solvent self-dissociation constant (in the -log10 representation)
*acid_type* = atom type of acid groups
*base_type* = atom type of base groups
*lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
@ -34,7 +34,7 @@ Syntax
*tempfixid* value = fix ID of temperature thermostat
*nevery* value = invoke this fix every nevery steps
*nmc* value = number of charge regulation MC moves to attempt every nevery steps
*xrd* value = cutoff distance for acid/base reaction
*rxd* value = cutoff distance for acid/base reaction
*seed* value = random # seed (positive integer)
*tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
*group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
@ -47,7 +47,7 @@ Examples
""""""""
.. code-block:: LAMMPS
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
@ -92,7 +92,11 @@ where the fix attempts to charge :math:`\mathrm{A}` (discharge
:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
insert (delete) a proton (atom type 2). Besides, the fix implements
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly
\mathrm{H}^++\mathrm{OH}^-`.
However, this approach is highly
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
both protons and hydroxyl ions is low, resulting in a relatively low
acceptance rate of MC moves.
@ -102,24 +106,31 @@ reactions, which can be easily achieved via
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
where particles of atom type 4 and 5 are the salt cations and anions,
both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) <Curk1>` and
:ref:`(Landsgesell) <Landsgesell>` for more details.
Similarly, we could have simultaneously added a base ionization reaction
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
.. code-block:: LAMMPS
fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
fix acid_base_reaction all charge/regulation 2 3 acid_type 1 base_type 6 pH 7.0 pKa 5.0 pKb 6.0 pIp 7.0 pIm 7.0
where the fix will attempt to charge :math:`\mathrm{B}` (discharge
:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If
neither the acid or the base type is specified, for example,
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.
Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) <Curk1>`. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read,
.. code-block:: LAMMPS
fix acid_reaction_combined all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 5.958 pIm 5.958
If neither the acid or the base type is specified, for example,
.. code-block:: LAMMPS
@ -127,11 +138,11 @@ neither the acid or the base type is specified, for example,
the fix simply inserts or deletes an ion pair of a free cation (atom
type 4) and a free anion (atom type 5) as done in a conventional
grand-canonical MC simulation.
grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword.
The fix is compatible with LAMMPS sub-packages such as *molecule* or
*rigid*. That said, the acid and base particles can be part of larger
*rigid*. The acid and base particles can be part of larger
molecules or rigid bodies. Free ions that are inserted to or deleted
from the system must be defined as single particles (no bonded
interactions allowed) and cannot be part of larger molecules or rigid
@ -153,14 +164,14 @@ Langevin thermostat:
fix fT all langevin 1.0 1.0 1.0 123
fix_modify fT temp dtemp
The chemical potential units (e.g. pH) are in the standard log10
The units of pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10
representation assuming reference concentration :math:`\rho_0 =
\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit
conversion, the length (in nanometers) of the LAMMPS unit length must be
specified via *lunit_nm* (default is set to the Bjerrum length in water
at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
ideal solution limit, the concentration of free ions will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
\mathrm{mol}/\mathrm{l}`. For example, in the dilute
ideal solution limit, the concentration of free cations will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit
conversion, the the value of the LAMMPS unit length must be
specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water
at room temperature (0.71 nm), *lunit_nm* = 0.71.
The temperature used in MC acceptance probability is set by *temp*. This
temperature should be the same as the temperature set by the molecular
@ -171,10 +182,10 @@ thermostat fix-ID is *fT*. The inserted particles attain a random
velocity corresponding to the specified temperature. Using *tempfixid*
overrides any fixed temperature set by *temp*.
The *xrd* keyword can be used to restrict the inserted/deleted
The *rxd* keyword can be used to restrict the inserted/deleted
counterions to a specific radial distance from an acid or base particle
that is currently participating in a reaction. This can be used to
simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
simulate more realist reaction dynamics. If *rxd* = 0 or *rxd* > *L* /
2, where *L* is the smallest box dimension, the radial restriction is
automatically turned off and free ion can be inserted or deleted
anywhere in the simulation box.
@ -258,18 +269,18 @@ Default
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
100; nmc = 100; rxd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
[1/3, 1/3, 1/3], group-ID = all
----------
.. _Curk1:
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Accelerated simulation method for charge regulation effects", JCP 156 (2022).
.. _Curk2:
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL 126 (2021)
.. _Landsgesell:

23
doc/src/fix_numdiff.rst
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@ -13,16 +13,15 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* numdiff = style name of this fix command
* Nevery = calculate force by finite difference every this many timesteps
* delta = finite difference displacement length (distance units)
* delta = size of atom displacements (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all numdiff 1 0.0001
fix 1 all numdiff 10 1e-6
fix 1 all numdiff 100 0.01
fix 1 movegroup numdiff 100 0.01
Description
"""""""""""
@ -67,16 +66,17 @@ by two times *delta*.
The cost of each energy evaluation is essentially the cost of an MD
timestep. Thus invoking this fix once for a 3d system has a cost
of 6N timesteps, where N is the total number of atoms in the system
(assuming all atoms are included in the group). So this fix can be
very expensive to use for large systems.
of 6N timesteps, where N is the total number of atoms in the system.
So this fix can be very expensive to use for large systems.
One expedient alternative is to define the fix for a group containing
only a few atoms.
----------
The *Nevery* argument specifies on what timesteps the force will
be used calculated by finite difference.
The *delta* argument specifies the positional displacement each
The *delta* argument specifies the size of the displacement each
atom will undergo.
----------
@ -93,7 +93,12 @@ This fix produces a per-atom array which can be accessed by various
the force on each atom as calculated by finite difference. The
per-atom values can only be accessed on timesteps that are multiples
of *Nevery* since that is when the finite difference forces are
calculated.
calculated. See the examples in *examples/numdiff* directory
to see how this fix can be used to directly compare with
the analytic forces computed by LAMMPS.
The array values calculated by this compute
will be in force :doc:`units <units>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
@ -108,7 +113,7 @@ was built with that package. See the :doc:`Build package <Build_package>` page
Related commands
""""""""""""""""
:doc:`dynamical_matrix <dynamical_matrix>`,
:doc:`dynamical_matrix <dynamical_matrix>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
Default
"""""""

115
doc/src/fix_numdiff_virial.rst Normal file
View File

@ -0,0 +1,115 @@
.. index:: fix numdiff/virial
fix numdiff/virial command
==========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID numdiff/virial Nevery delta
* ID, group-ID are documented in :doc:`fix <fix>` command
* numdiff/virial = style name of this fix command
* Nevery = calculate virial by finite difference every this many timesteps
* delta = magnitude of strain fields (dimensionless)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all numdiff/stress 10 1e-6
Description
"""""""""""
Calculate the virial stress tensor through a finite difference calculation of
energy versus strain. These values can be compared to the analytic virial
tensor computed by pair styles, bond styles, etc. This can be useful for
debugging or other purposes. The specified group must be "all".
This fix applies linear strain fields of magnitude *delta* to all the
atoms relative to a point at the center of the box. The
strain fields are in six different directions, corresponding to the
six Cartesian components of the stress tensor defined by LAMMPS.
For each direction it applies the strain field in both the positive
and negative senses, and the new energy of the entire system
is calculated after each. The difference in these two energies
divided by two times *delta*, approximates the corresponding
component of the virial stress tensor, after applying
a suitable unit conversion.
.. note::
It is important to choose a suitable value for delta, the magnitude of
strains that are used to generate finite difference
approximations to the exact virial stress. For typical systems, a value in
the range of 1 part in 1e5 to 1e6 will be sufficient.
However, the best value will depend on a multitude of factors
including the stiffness of the interatomic potential, the thermodynamic
state of the material being probed, and so on. The only way to be sure
that you have made a good choice is to do a sensitivity study on a
representative atomic configuration, sweeping over a wide range of
values of delta. If delta is too small, the output values will vary
erratically due to truncation effects. If delta is increased beyond a
certain point, the output values will start to vary smoothly with
delta, due to growing contributions from higher order derivatives. In
between these two limits, the numerical virial values should be largely
independent of delta.
----------
The *Nevery* argument specifies on what timesteps the force will
be used calculated by finite difference.
The *delta* argument specifies the size of the displacement each
atom will undergo.
----------
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 produces a global vector which can be accessed by various
:doc:`output commands <Howto_output>`, which stores the components of
the virial stress tensor as calculated by finite difference. The
global vector can only be accessed on timesteps that are multiples
of *Nevery* since that is when the finite difference virial is
calculated. See the examples in *examples/numdiff* directory
to see how this fix can be used to directly compare with
the analytic virial stress tensor computed by LAMMPS.
The order of the virial stress tensor components is *xx*, *yy*, *zz*,
*yz*, *xz*, and *xy*, consistent with Voigt notation. Note that
the vector produced by :doc:`compute pressure <compute_pressure>`
uses a different ordering, with *yz* and *xy* swapped.
The vector values calculated by this compute are
"intensive". The vector values will be in pressure
:doc:`units <units>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix numdiff <fix_numdiff>`, :doc:`compute pressure <compute_pressure>`
Default
"""""""
none

9
doc/src/fix_nvt_sllod.rst
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@ -66,7 +66,10 @@ equivalent to Newton's equations of motion for shear flow by
:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
the desired velocity gradient and the correct production of work by
stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
<Daivis>`. As implemented in LAMMPS, they are coupled to a
<Daivis>`.
The LAMMPS implementation corresponds to the p-SLLOD variant
of SLLOD. :ref:`(Edwards) <Edwards>`.
The equations of motion are coupled to a
Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
following the implementation used for the :doc:`fix nvt <fix_nh>`
command.
@ -180,6 +183,10 @@ Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
.. _Edwards:
**(Edwards)** Edwards, Baig, and Keffer, J Chem Phys 124, 194104 (2006).
.. _Daivis-sllod:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),

9
doc/src/fix_viscosity.rst
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@ -108,10 +108,11 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper <Muller-Plathe2>
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described on the :doc:`Howto nemd <Howto_nemd>` doc page.
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command. Thus they cannot be run on a charged
system using a :doc:`PPPM solver <kspace_style>` since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
box orthogonal; thus it does not suffer from this limitation.
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command.
Some features or combination of settings in LAMMPS do not support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
thus it does not suffer from these limitations.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/package.rst
View File

@ -460,7 +460,7 @@ using *neigh/thread* *on*, a full neighbor list must also be used. Using
is turned on by default only when there are 16K atoms or less owned by
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
potentials support this keyword yet, and only thread over atoms. Many
simple pair-wise potentials such as Lennard-Jones do support threading
simple pairwise potentials such as Lennard-Jones do support threading
over both atoms and neighbors.
The *newton* keyword sets the Newton flags for pairwise and bonded

2
doc/src/pair_charmm.rst
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@ -119,7 +119,7 @@ name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
shown in the formula below as S(r)), which ramps the energy smoothly
to zero between the inner and outer cutoff. This can cause
irregularities in pair-wise forces (due to the discontinuous second
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.

2
doc/src/pair_dpd.rst
View File

@ -50,7 +50,7 @@ Style *dpd* computes a force field for dissipative particle dynamics
Style *dpd/tstat* invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This pair-wise thermostat can be used in conjunction with any
field. This pairwise thermostat can be used in conjunction with any
:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use

90
doc/src/pair_harmonic_cut.rst Normal file
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@ -0,0 +1,90 @@
.. index:: pair_style harmonic/cut
.. index:: pair_style harmonic/cut/omp
pair_style harmonic/cut command
===============================
Accelerator Variants: *harmonic/cut/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
* style = *harmonic/cut*
Examples
""""""""
.. code-block:: LAMMPS
pair_style harmonic/cut 2.5
pair_coeff * * 0.2 2.0
pair_coeff 1 1 0.5 2.5
Description
"""""""""""
Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with the formula
.. math::
E = k (r_c - r)^2 \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:`k` (energy units)
* :math:`r_c` (distance units)
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the :math:`k` and :math:`r_c`
coefficients can be mixed. The default mix value is *geometric*.
See the "pair_modify" command for details.
Since the potential is zero at and beyond the cutoff parameter by
construction, there is no need to support support the :doc:`pair_modify
<pair_modify>` shift or tail options for the energy and pressure of the
pair interaction.
These pair styles write their information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands do not need to be specified in an input script
that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
The *harmonic/cut* 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>`
Default
"""""""
none

2
doc/src/pair_ilp_graphene_hbn.rst
View File

@ -159,6 +159,8 @@ Related commands
:doc:`pair_none <pair_none>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style drip <pair_drip>`,
:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
:doc:`pair_style saip_metal <pair_saip_metal>`,
:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,

157
doc/src/pair_ilp_tmd.rst Normal file
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@ -0,0 +1,157 @@
.. index:: pair_style ilp/tmd
pair_style ilp/tmd command
===================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] ilp/tmd cutoff tap_flag
* cutoff = global cutoff (distance units)
* tap_flag = 0/1 to turn off/on the taper function
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay ilp/tmd 16.0 1
pair_coeff * * ilp/tmd TMD.ILP Mo S S
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd TMD.ILP Mo S S Mo S S
Description
"""""""""""
The *ilp/tmd* style computes the registry-dependent interlayer
potential (ILP) potential for transition metal dichalcogenides (TMD)
as described in :ref:`(Ouyang7) <Ouyang7>`.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
a continuous cutoff (up to third derivative) for interatomic separations
larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
.. note::
Since each MX2 (M = Mo, W and X = S, Se Te) layer contains two
sub-layers of X atoms and one sub-layer of M atoms, the definition of the
normal vectors used for graphene and h-BN is no longer valid for TMDs.
In :ref:`(Ouyang7) <Ouyang7>`, a new definition is proposed, where for
each atom `i`, its six nearest neighboring atoms belonging to the same
sub-layer are chosen to define the normal vector `{\bf n}_i`.
The parameter file (e.g. TMD.ILP), is intended for use with *metal*
:doc:`units <units>`, with energies in meV. Two additional parameters,
*S*, and *rcut* are included in the parameter file. *S* is designed to
facilitate scaling of energies. *rcut* is designed to build the neighbor
list for calculating the normals for each atom pair.
.. note::
The parameters presented in the parameter file (e.g. TMD.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
These parameters provide a good description in both short- and long-range
interaction regimes. This feature is essential for simulations in high pressure
regime (i.e., the interlayer distance is smaller than the equilibrium
distance). The benchmark tests and comparison of these parameters can
be found in :ref:`(Ouyang7) <Ouyang7>`.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style *none*\ .
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
1. *E_vdW* = vdW (attractive) energy
2. *E_Rep* = Repulsive energy
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute 0 all pair ilp/tmd
variable Evdw equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step temp epair v_Erep v_Evdw
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support the pair_modify mix, shift, table, and
tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
Restrictions
""""""""""""
This pair style is part of the INTERLAYER package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the newton setting to be *on* for pair
interactions.
The TMD.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_none <pair_none>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style drip <pair_drip>`,
:doc:`pair_style saip_metal <pair_saip_metal>`,
:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
Default
"""""""
tap_flag = 1
----------
.. _Ouyang7:
**(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).

2
doc/src/pair_python.rst
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@ -164,7 +164,7 @@ Following the *LJCutMelt* example, here are the two functions:
.. note::
The evaluation of scripted python code will slow down the
computation pair-wise interactions quite significantly. However, this
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below

156
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@ -0,0 +1,156 @@
.. index:: pair_style saip/metal
pair_style saip/metal command
===================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] saip/metal cutoff tap_flag
* cutoff = global cutoff (distance units)
* tap_flag = 0/1 to turn off/on the taper function
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay saip/metal 16.0 1
pair_coeff * * saip/metal CHAu.ILP Au C H
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam Au_u3.eam Au NULL NULL
pair_coeff * * rebo CH.rebo NULL C H
pair_coeff * * saip/metal CHAu.ILP Au C H
Description
"""""""""""
The *saip/metal* style computes the registry-dependent interlayer
potential (ILP) potential for hetero-junctions formed with hexagonal
2D materials and metal surfaces, as described in :ref:`(Ouyang6) <Ouyang6>`.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
a continuous cutoff (up to third derivative) for interatomic separations
larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
.. note::
To account for the isotropic nature of the isolated gold atom
electron cloud, their corresponding normal vectors (`{\bf n}_i`) are
assumed to lie along the interatomic vector `{\bf r}_ij`. Notably, this
assumption is suitable for many bulk material surfaces, for
example, for systems possessing s-type valence orbitals or
metallic surfaces, whose valence electrons are mostly
delocalized, such that their Pauli repulsion with the electrons
of adjacent surfaces are isotropic. Caution should be used in
the case of very small gold contacts, for example, nano-clusters,
where edge effects may become relevant.
The parameter file (e.g. CHAu.ILP), is intended for use with *metal*
:doc:`units <units>`, with energies in meV. Two additional parameters,
*S*, and *rcut* are included in the parameter file. *S* is designed to
facilitate scaling of energies. *rcut* is designed to build the neighbor
list for calculating the normals for each atom pair.
.. note::
The parameters presented in the parameter file (e.g. BNCH.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style *none*\ .
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
1. *E_vdW* = vdW (attractive) energy
2. *E_Rep* = Repulsive energy
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute 0 all pair saip/metal
variable Evdw equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step temp epair v_Erep v_Evdw
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support the pair_modify mix, shift, table, and
tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
Restrictions
""""""""""""
This pair style is part of the INTERLAYER package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the newton setting to be *on* for pair
interactions.
The CHAu.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_none <pair_none>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style drip <pair_drip>`,
:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
Default
"""""""
tap_flag = 1
----------
.. _Ouyang6:
**(Ouyang6)** W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).

7
doc/src/pair_style.rst
View File

@ -154,10 +154,10 @@ accelerated styles exist.
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting
* :doc:`dpd/tstat <pair_dpd>` - pairwise DPD thermostatting
* :doc:`dsmc <pair_dsmc>` - Direct Simulation Monte Carlo (DSMC)
* :doc:`e3b <pair_e3b>` - Explicit-three body (E3B) water model
* :doc:`drip <pair_drip>` - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
@ -183,10 +183,12 @@ accelerated styles exist.
* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
* :doc:`gw <pair_gw>` - Gao-Weber potential
* :doc:`gw/zbl <pair_gw>` - Gao-Weber potential with a repulsive ZBL core
* :doc:`harmonic/cut <pair_harmonic_cut>` - repulsive-only harmonic potential
* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`ilp/tmd <pair_ilp_tmd>` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
@ -304,6 +306,7 @@ accelerated styles exist.
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`smd/hertz <pair_smd_hertz>` -
* :doc:`smd/tlsph <pair_smd_tlsph>` -

10
doc/src/pair_sw.rst
View File

@ -29,8 +29,8 @@ Syntax
.. parsed-literal::
*maxdelcs* value = delta1 delta2 (optional)
delta1 = The minimum thershold for cosine of three-body angle
delta2 = The maximum threshold for cosine of three-body angle
delta1 = The minimum thershold for the variation of cosine of three-body angle
delta2 = The maximum threshold for the variation of cosine of three-body angle
Examples
""""""""
@ -69,7 +69,7 @@ and K of atom I within a cutoff distance :math:`a `\sigma`.
The *sw/mod* style is designed for simulations of materials when
distinguishing three-body angles are necessary, such as borophene
and transition metal dichalcogenide, which cannot be described
and transition metal dichalcogenides, which cannot be described
by the original code for the Stillinger-Weber potential.
For instance, there are several types of angles around each Mo atom in `MoS_2`,
and some unnecessary angle types should be excluded in the three-body interaction.
@ -99,7 +99,7 @@ This smoothly turns off the energy and force contributions for :math:`\left| \de
It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around
:math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with
:math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom.
For borophene and transition metal dichalcogenide, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`.
For borophene and transition metal dichalcogenides, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`.
This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms.
.. note::
@ -202,7 +202,7 @@ elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
are usually defined by simple formulas involving two sets of pairwise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the three-body parameters for

6
doc/src/pair_write.rst
View File

@ -76,8 +76,10 @@ must be set before this command can be invoked.
Due to how the pairwise force is computed, an inner value > 0.0 must
be specified even if the potential has a finite value at r = 0.0.
For EAM potentials, the pair_write command only tabulates the
pairwise portion of the potential, not the embedding portion.
The *pair_write* command can only be used for pairwise additive
interactions for which a `Pair::single()` function can be and has
been implemented. This excludes for example manybody potentials
or TIP4P coulomb styles.
Related commands
""""""""""""""""

2
doc/src/run_style.rst
View File

@ -89,7 +89,7 @@ in its 3d FFTs. In this scenario, splitting your P total processors
into 2 subsets of 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 pair-wise and bonded forces are being calculated, and the FFTs
time as pairwise and bonded forces are being calculated, and the FFTs
can actually speed up when running on fewer processors.
To use this style, you must define 2 partitions where P1 is a multiple

9
doc/src/third_order.rst
View File

@ -1,8 +1,11 @@
.. index:: third_order
.. index:: third_order/kk
third_order command
===================
Accelerator Variants: third_order/kk
Syntax
""""""
@ -49,6 +52,12 @@ If the style eskm is selected, the tensor will be using energy units of 10 J/mol
These units conform to eskm style from the dynamical_matrix command, which
will simplify operations using dynamical matrices with third order tensors.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

2
doc/utils/check-styles.py
View File

@ -259,7 +259,7 @@ skip_pair = ('meam/c','lj/sf','reax/c')
counter = 0
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=False)
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=True)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)

242
doc/utils/sphinx-config/false_positives.txt
View File

File diff suppressed because it is too large Load Diff

249
examples/PACKAGES/cgdna/examples/test.sh
View File

@ -1,20 +1,24 @@
#! /bin/bash
DATE='2Jul21'
LMPDIR=/Users/ohenrich/Work/code/lammps
DATE='14Dec21'
TOL=1e-8
LMPDIR=/Users/ohenrich/Work/code/lammps
SRCDIR=$LMPDIR/src
EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples
if [ $# -eq 1 ] && [ $1 = run ]; then
echo '# Compiling executable in' $SRCDIR
echo '# Compiling executable in' $SRCDIR | tee -a $EXDIR/test.log
cd $SRCDIR
make clean-all
make -j8 mpi
make clean-all | tee -a $EXDIR/test.log
make purge | tee -a $EXDIR/test.log
make pu | tee -a $EXDIR/test.log
make ps | tee -a $EXDIR/test.log
make -j8 mpi | tee -a $EXDIR/test.log
######################################################
echo '# Running oxDNA duplex1 test'
echo '# Running oxDNA duplex1 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA/duplex1
mkdir test
cd test
@ -24,20 +28,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.1
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex1.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.4
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex1.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA duplex2 test'
echo '# Running oxDNA duplex2 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA/duplex2
mkdir test
cd test
@ -47,20 +63,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA2 duplex1 test'
echo '# Running oxDNA2 duplex1 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA2/duplex1
mkdir test
cd test
@ -70,20 +98,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.1
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex1.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.4
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex1.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA2 duplex2 test'
echo '# Running oxDNA2 duplex2 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA2/duplex2
mkdir test
cd test
@ -93,20 +133,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA2 duplex3 test'
echo '# Running oxDNA2 duplex3 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA2/duplex3
mkdir test
cd test
@ -116,20 +168,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null
mv log.lammps log.$DATE.duplex3.g++.1
grep etot log.$DATE.duplex3.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex3.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null
mv log.lammps log.$DATE.duplex3.g++.4
grep etot log.$DATE.duplex3.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex3.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA2 unique_bp test'
echo '# Running oxDNA2 unique_bp test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA2/unique_bp
mkdir test
cd test
@ -141,32 +205,56 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null
mv log.lammps log.$DATE.duplex4.4type.g++.1
grep etot log.$DATE.duplex4.4type.g++.1 > e_test.dat
grep etot ../log*4type*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex4.4type.g++.1 > e_test.4type.1.dat
grep etot ../log*4type*1 > e_old.4type.1.dat
ndiff -relerr $TOL e_test.4type.1.dat e_old.4type.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task 4 types passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task 4 types unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null
mv log.lammps log.$DATE.duplex4.4type.g++.4
grep etot log.$DATE.duplex4.4type.g++.4 > e_test.dat
grep etot ../log*4type*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex4.4type.g++.4 > e_test.4type.4.dat
grep etot ../log*4type*4 > e_old.4type.4.dat
ndiff -relerr $TOL e_test.4type.4.dat e_old.4type.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks 4 types passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks 4 types unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null
mv log.lammps log.$DATE.duplex4.8type.g++.1
grep etot log.$DATE.duplex4.8type.g++.1 > e_test.dat
grep etot ../log*8type*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex4.8type.g++.1 > e_test.8type.1.dat
grep etot ../log*8type*1 > e_old.8type.1.dat
ndiff -relerr $TOL e_test.8type.1.dat e_old.8type.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task 8 types passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task 8 types unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null
mv log.lammps log.$DATE.duplex4.8type.g++.4
grep etot log.$DATE.duplex4.8type.g++.4 > e_test.dat
grep etot ../log*8type*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex4.8type.g++.4 > e_test.8type.4.dat
grep etot ../log*8type*4 > e_old.8type.4.dat
ndiff -relerr $TOL e_test.8type.4.dat e_old.8type.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks 8 types passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks 8 types unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxDNA2 dsring test'
echo '# Running oxDNA2 dsring test' | tee -a $EXDIR/test.log
cd $EXDIR/oxDNA2/dsring
mkdir test
cd test
@ -176,20 +264,32 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null
mv log.lammps log.$DATE.dsring.g++.1
grep etot log.$DATE.dsring.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.dsring.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null
mv log.lammps log.$DATE.dsring.g++.4
grep etot log.$DATE.dsring.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.dsring.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
######################################################
echo '# Running oxRNA2 duplex2 test'
echo '# Running oxRNA2 duplex2 test' | tee -a $EXDIR/test.log
cd $EXDIR/oxRNA2/duplex2
mkdir test
cd test
@ -199,18 +299,30 @@ if [ $# -eq 1 ] && [ $1 = run ]; then
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.1 > e_test.1.dat
grep etot ../log*1 > e_old.1.dat
ndiff -relerr $TOL e_test.1.dat e_old.1.dat
if [ $? -eq 0 ];
then
echo "# 1 MPI-task passed" | tee -a $EXDIR/test.log
else
echo "# 1 MPI-task unsuccessful" | tee -a $EXDIR/test.log
fi
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
grep etot log.$DATE.duplex2.g++.4 > e_test.4.dat
grep etot ../log*4 > e_old.4.dat
ndiff -relerr $TOL e_test.4.dat e_old.4.dat
if [ $? -eq 0 ];
then
echo "# 4 MPI-tasks passed" | tee -a $EXDIR/test.log
else
echo "# 4 MPI-tasks unsuccessful" | tee -a $EXDIR/test.log
fi
######################################################
echo '# Done'
echo '# Done' | tee -a $EXDIR/test.log
elif [ $# -eq 1 ] && [ $1 = clean ]; then
echo '# Deleting test directories'
@ -222,6 +334,7 @@ elif [ $# -eq 1 ] && [ $1 = clean ]; then
rm -rf $EXDIR/oxDNA2/unique_bp/test
rm -rf $EXDIR/oxDNA2/dsring/test
rm -rf $EXDIR/oxRNA2/duplex2/test
rm -rf $EXDIR/test.log
echo '# Done'
else

4
examples/PACKAGES/electron_stopping/Si.Si.elstop
View File

@ -1,8 +1,8 @@
# Electronic stopping for Si in Si
# Uses metal units
# Electronic stopping for Si in Si UNITS: metal DATE: 2019-02-19 CONTRIBUTOR: Risto Toijala risto.toijala@helsinki.fi
# Kinetic energy in eV, stopping power in eV/A
# For other atom types, add columns.
# atom type 1
# energy Si in Si
3918.2 6.541
15672.9 13.091

2
examples/PACKAGES/gle/qt-300k.A
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
3.904138445158e-4 4.681059722010e-2 3.079778738058e-2 4.428079381336e-2 5.057825203477e-2 2.591193419597e-2 1.513907125942e-2
-4.789343294190e-2 2.037551040972e-2 6.597801861779e-2 -8.528273506602e-3 -2.230839572773e-3 6.593086307870e-3 -6.653653981891e-2
-2.905096373618e-2 -6.597801861779e-2 2.086885297843e-2 1.145471984072e-2 3.111465343867e-2 1.101562087523e-2 -3.264959166486e-2

2
examples/PACKAGES/gle/qt-300k.C
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
2.999985914100e+2 5.937593337000e+0 2.144376751500e+2 5.883055908000e+1 -1.119803766000e+2 -6.793381764000e+1 1.379789732400e+1
5.937593337000e+0 3.781851303000e+2 -5.794518522000e+1 -2.178772681500e+2 -1.649310659100e+2 -6.557113452000e+1 3.833830743000e+1
2.144376751500e+2 -5.794518522000e+1 7.325759985000e+2 2.188507713000e+2 -3.704586531000e+2 -3.385193865000e+1 -4.827706758000e+0

2
examples/PACKAGES/gle/smart.A
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
4.247358737218e-3 3.231404593065e-2 -9.715629522215e-3 8.199488441225e-3 7.288427565896e-3 -3.634229949055e-3 -3.294395982200e-3
4.887738278128e-2 5.978602802893e-1 -2.079222967202e-1 1.088740438247e-1 4.666954324786e-2 -1.334147134493e-2 -3.914996645811e-2
4.015863091190e-2 2.079222967202e-1 1.645970119444e-1 8.351952991453e-2 5.114740085468e-2 1.217862237677e-2 -4.506711205974e-2

1
examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH.ILP Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/BNCH.ILP

1
examples/PACKAGES/interlayer/ilp_graphene_hbn/CH.rebo Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/CH.rebo

1
examples/PACKAGES/interlayer/ilp_tmds/MoS2.ILP Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/MoS2.ILP

1549
examples/PACKAGES/interlayer/ilp_tmds/bilayer_MoS2_AAprime_stacking.data Normal file
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File diff suppressed because it is too large Load Diff

36
examples/PACKAGES/interlayer/ilp_tmds/in.mos2 Normal file
View File

@ -0,0 +1,36 @@
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000

154
examples/PACKAGES/interlayer/ilp_tmds/log.7Jan22.mos2.g++.1 Normal file
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@ -0,0 +1,154 @@
LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1536 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.007 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
Reading ilp/tmd potential file MoS2.ILP with DATE: 2021-12-02
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 9 5 23
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/tmd, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 30.29 | 30.29 | 30.29 Mbytes
Step TotEng PotEng KinEng v_SW1 v_SW2 v_ILP v_Erep v_Eatt Temp
0 -1834.4469 -1893.9712 59.524297 -929.02881 -929.02881 -35.913549 63.00343 -98.916979 300
100 -1834.4497 -1883.3105 48.860775 -924.84264 -925.08505 -33.382796 56.58255 -89.965346 246.25629
200 -1834.4381 -1873.7072 39.269085 -922.29961 -922.52535 -28.882252 50.08277 -78.965022 197.91457
300 -1834.4483 -1881.1263 46.678028 -923.39264 -923.65627 -34.077402 51.011967 -85.089369 235.25534
400 -1834.431 -1868.0728 33.64182 -916.85743 -916.27044 -34.944916 50.414038 -85.358954 169.55338
500 -1834.4499 -1881.9059 47.456 -925.22919 -924.29582 -32.380877 44.755168 -77.136045 239.17628
600 -1834.4343 -1869.8642 35.429976 -920.97805 -919.60784 -29.278358 43.270241 -72.548599 178.56562
700 -1834.443 -1878.144 43.700934 -921.8051 -921.55671 -34.782141 49.959943 -84.742084 220.2509
800 -1834.4327 -1869.824 35.391298 -917.19193 -917.91383 -34.718247 55.349728 -90.067976 178.37068
900 -1834.4465 -1877.6741 43.227638 -923.33877 -922.50874 -31.826599 53.965592 -85.792191 217.86551
1000 -1834.4412 -1876.1808 41.739587 -923.17282 -923.49367 -29.514347 55.454643 -84.96899 210.3658
Loop time of 72.8218 on 1 procs for 1000 steps with 1536 atoms
Performance: 1.186 ns/day, 20.228 hours/ns, 13.732 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 72.781 | 72.781 | 72.781 | 0.0 | 99.94
Bond | 0.00014503 | 0.00014503 | 0.00014503 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016691 | 0.016691 | 0.016691 | 0.0 | 0.02
Output | 0.00057989 | 0.00057989 | 0.00057989 | 0.0 | 0.00
Modify | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.02
Other | | 0.01044 | | | 0.01
Nlocal: 1536 ave 1536 max 1536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3510 ave 3510 max 3510 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 992256 ave 992256 max 992256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 992256
Ave neighs/atom = 646
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:12

154
examples/PACKAGES/interlayer/ilp_tmds/log.7Jan22.mos2.g++.4 Normal file
View File

@ -0,0 +1,154 @@
LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./bilayer_MoS2_AAprime_stacking.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
2 by 2 by 1 MPI processor grid
reading atoms ...
1536 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass 4 95.94
# Define potentials
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
Reading ilp/tmd potential file MoS2.ILP with DATE: 2021-12-02
# Calculate the pair potential
compute 0 all pair ilp/tmd
compute 1 all pair sw/mod 1
compute 2 all pair sw/mod 2
variable SW1 equal c_1
variable SW2 equal c_2
variable ILP equal c_0
variable Eatt equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step etotal pe ke v_SW1 v_SW2 v_ILP v_Erep v_Eatt temp
thermo 100
thermo_modify lost error
timestep 1e-3
velocity all create 300.0 12345
fix intall all nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7237–7245}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 9 5 23
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair sw/mod, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/tmd, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.98 | 17.98 | 17.98 Mbytes
Step TotEng PotEng KinEng v_SW1 v_SW2 v_ILP v_Erep v_Eatt Temp
0 -1834.4469 -1893.9712 59.524297 -929.02881 -929.02881 -35.913549 63.00343 -98.916979 300
100 -1834.4497 -1883.3105 48.860775 -924.84264 -925.08505 -33.382796 56.58255 -89.965346 246.25629
200 -1834.4381 -1873.7072 39.269085 -922.29961 -922.52535 -28.882252 50.08277 -78.965022 197.91457
300 -1834.4483 -1881.1263 46.678028 -923.39264 -923.65627 -34.077402 51.011967 -85.089369 235.25534
400 -1834.431 -1868.0728 33.64182 -916.85743 -916.27044 -34.944916 50.414038 -85.358954 169.55338
500 -1834.4499 -1881.9059 47.456 -925.22919 -924.29582 -32.380877 44.755168 -77.136045 239.17628
600 -1834.4343 -1869.8642 35.429976 -920.97805 -919.60784 -29.278358 43.270241 -72.548599 178.56562
700 -1834.443 -1878.144 43.700934 -921.8051 -921.55671 -34.782141 49.959943 -84.742084 220.2509
800 -1834.4327 -1869.824 35.391298 -917.19193 -917.91383 -34.718247 55.349728 -90.067976 178.37068
900 -1834.4465 -1877.6741 43.227638 -923.33877 -922.50874 -31.826599 53.965592 -85.792191 217.86551
1000 -1834.4412 -1876.1808 41.739587 -923.17282 -923.49367 -29.514347 55.454643 -84.96899 210.3658
Loop time of 24.6309 on 4 procs for 1000 steps with 1536 atoms
Performance: 3.508 ns/day, 6.842 hours/ns, 40.599 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.906 | 23.627 | 24.36 | 14.0 | 95.92
Bond | 0.00010889 | 0.00011572 | 0.00012719 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.25886 | 0.992 | 1.7126 | 68.3 | 4.03
Output | 0.00050901 | 0.00054202 | 0.00062029 | 0.0 | 0.00
Modify | 0.0030735 | 0.0033236 | 0.0035581 | 0.3 | 0.01
Other | | 0.008194 | | | 0.03
Nlocal: 384 ave 387 max 381 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 2262 ave 2265 max 2259 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 248064 ave 250002 max 246126 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 992256
Ave neighs/atom = 646
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:24

143
examples/PACKAGES/interlayer/ilp_tmds/tmd.sw.mod Normal file
View File

@ -0,0 +1,143 @@
# DATE: 2018-03-26 UNITS: metal CONTRIBUTOR: Jin-Wu Jiang jwjiang5918@hotmail.com
# CITATION: J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
# The Stillinger-Weber parameters, for transition-metal dichalcogenide (TMD) lateral heterostructures.
# M = Mo, W; X = S, Se, Te
# these entries are in LAMMPS "metal" units:
# epsilon = eV; sigma = Angstroms
# other quantities are unitless
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
# M-X-X terms
Mo S S 1.000 1.252 2.523 67.883 1.000 0.143 6.918 7.223 4 0 0.0
Mo Se Se 1.000 0.913 3.672 32.526 1.000 0.143 5.737 27.084 4 0 0.0
Mo Te Te 1.000 0.880 4.097 23.705 1.000 0.143 5.086 40.810 4 0 0.0
W S S 1.000 0.889 3.558 37.687 1.000 0.143 5.664 24.525 4 0 0.0
W Se Se 1.000 0.706 4.689 25.607 1.000 0.143 5.476 65.662 4 0 0.0
W Te Te 1.000 0.778 4.632 21.313 1.000 0.143 4.326 62.148 4 0 0.0
# X-M-M terms
S Mo Mo 1.000 1.252 2.523 62.449 1.000 0.143 6.918 7.223 4 0 0.0
S W W 1.000 0.889 3.558 33.553 1.000 0.143 5.664 24.525 4 0 0.0
Se Mo Mo 1.000 0.913 3.672 27.079 1.000 0.143 5.737 27.084 4 0 0.0
Se W W 1.000 0.706 4.689 23.218 1.000 0.143 5.476 65.662 4 0 0.0
Te Mo Mo 1.000 0.880 4.097 20.029 1.000 0.143 5.086 40.810 4 0 0.0
Te W W 1.000 0.778 4.632 17.370 1.000 0.143 4.326 62.148 4 0 0.0
# M-X1-X2 terms
Mo S Se 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo S Te 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se S 1.000 0.000 0.000 46.989 1.000 0.143 0.000 0.000 4 0 0.0
Mo Se Te 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te S 1.000 0.000 0.000 40.114 1.000 0.143 0.000 0.000 4 0 0.0
Mo Te Se 1.000 0.000 0.000 27.767 1.000 0.143 0.000 0.000 4 0 0.0
W S Se 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W S Te 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Se S 1.000 0.000 0.000 31.065 1.000 0.143 0.000 0.000 4 0 0.0
W Se Te 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
W Te S 1.000 0.000 0.000 28.341 1.000 0.143 0.000 0.000 4 0 0.0
W Te Se 1.000 0.000 0.000 23.362 1.000 0.143 0.000 0.000 4 0 0.0
# X-M1-M2 terms
S Mo W 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
S W Mo 1.000 0.000 0.000 45.775 1.000 0.143 0.000 0.000 4 0 0.0
Se Mo W 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Se W Mo 1.000 0.000 0.000 25.074 1.000 0.143 0.000 0.000 4 0 0.0
Te Mo W 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
Te W Mo 1.000 0.000 0.000 18.652 1.000 0.143 0.000 0.000 4 0 0.0
# zero terms
Mo Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Mo Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
W Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
S Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Se Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Mo Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te W Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te S Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Se Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Mo 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te W 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te S 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Se 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0
Te Te Te 0.000 1.000 1.000 1.000 1.000 0.143 1.000 1.000 4 0 0.0

218
examples/PACKAGES/interlayer/saip_metal/3Lgold_1Lgr_atop_sliding.data Normal file
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Gold/graphene heterjunction atop2
206 atoms
2 atom types
0 17.216640 xlo xhi
0 14.910048 ylo yhi
-30 30.000000 zlo zhi
8.60832 0 0 xy xz yz
Atoms
1 1 1 0 -8.60832 -4.97002 3.5
2 1 1 0 -7.1736 -4.14166 5.85461
3 1 1 0 -5.73888 -3.31334 8.20922
4 1 1 0 -7.1736 -2.48501 3.5
5 1 1 0 -5.73888 -1.65666 5.85461
6 1 1 0 -4.30416 -0.828336 8.20922
7 1 1 0 -5.73888 0 3.5
8 1 1 0 -4.30416 0.828352 5.85461
9 1 1 0 -2.86944 1.65667 8.20922
10 1 1 0 -4.30416 2.48501 3.5
11 1 1 0 -2.86944 3.31336 5.85461
12 1 1 0 -1.43472 4.14168 8.20922
13 1 1 0 -2.86944 4.97002 3.5
14 1 1 0 -1.43472 5.79837 5.85461
15 1 1 0 0 6.62669 8.20922
16 1 1 0 -1.43472 7.45502 3.5
17 1 1 0 0 8.28337 5.85461
18 1 1 0 1.43472 9.11167 8.20922
19 1 1 0 -5.73888 -4.97002 3.5
20 1 1 0 -4.30416 -4.14166 5.85461
21 1 1 0 -2.86944 -3.31334 8.20922
22 1 1 0 -4.30416 -2.48501 3.5
23 1 1 0 -2.86944 -1.65666 5.85461
24 1 1 0 -1.43472 -0.828336 8.20922
25 1 1 0 -2.86944 0 3.5
26 1 1 0 -1.43472 0.828352 5.85461
27 1 1 0 0 1.65667 8.20922
28 1 1 0 -1.43472 2.48501 3.5
29 1 1 0 0 3.31336 5.85461
30 1 1 0 1.43472 4.14168 8.20922
31 1 1 0 0 4.97002 3.5
32 1 1 0 1.43472 5.79837 5.85461
33 1 1 0 2.86944 6.62669 8.20922
34 1 1 0 1.43472 7.45502 3.5
35 1 1 0 2.86944 8.28337 5.85461
36 1 1 0 4.30416 9.11167 8.20922
37 1 1 0 -2.86944 -4.97002 3.5
38 1 1 0 -1.43472 -4.14166 5.85461
39 1 1 0 0 -3.31334 8.20922
40 1 1 0 -1.43472 -2.48501 3.5
41 1 1 0 0 -1.65666 5.85461
42 1 1 0 1.43472 -0.828336 8.20922
43 1 1 0 0 0 3.5
44 1 1 0 1.43472 0.828352 5.85461
45 1 1 0 2.86944 1.65667 8.20922
46 1 1 0 1.43472 2.48501 3.5
47 1 1 0 2.86944 3.31336 5.85461
48 1 1 0 4.30416 4.14168 8.20922
49 1 1 0 2.86944 4.97002 3.5
50 1 1 0 4.30416 5.79837 5.85461
51 1 1 0 5.73888 6.62669 8.20922
52 1 1 0 4.30416 7.45502 3.5
53 1 1 0 5.73888 8.28337 5.85461
54 1 1 0 7.1736 9.11167 8.20922
55 1 1 0 0 -4.97002 3.5
56 1 1 0 1.43472 -4.14166 5.85461
57 1 1 0 2.86944 -3.31334 8.20922
58 1 1 0 1.43472 -2.48501 3.5
59 1 1 0 2.86944 -1.65666 5.85461
60 1 1 0 4.30416 -0.828336 8.20922
61 1 1 0 2.86944 0 3.5
62 1 1 0 4.30416 0.828352 5.85461
63 1 1 0 5.73888 1.65667 8.20922
64 1 1 0 4.30416 2.48501 3.5
65 1 1 0 5.73888 3.31336 5.85461
66 1 1 0 7.1736 4.14168 8.20922
67 1 1 0 5.73888 4.97002 3.5
68 1 1 0 7.1736 5.79837 5.85461
69 1 1 0 8.60832 6.62669 8.20922
70 1 1 0 7.1736 7.45502 3.5
71 1 1 0 8.60832 8.28337 5.85461
72 1 1 0 10.0431 9.11167 8.20922
73 1 1 0 2.86944 -4.97002 3.5
74 1 1 0 4.30416 -4.14166 5.85461
75 1 1 0 5.73888 -3.31334 8.20922
76 1 1 0 4.30416 -2.48501 3.5
77 1 1 0 5.73888 -1.65666 5.85461
78 1 1 0 7.1736 -0.828336 8.20922
79 1 1 0 5.73888 0 3.5
80 1 1 0 7.1736 0.828352 5.85461
81 1 1 0 8.60832 1.65667 8.20922
82 1 1 0 7.1736 2.48501 3.5
83 1 1 0 8.60832 3.31336 5.85461
84 1 1 0 10.0431 4.14168 8.20922
85 1 1 0 8.60832 4.97002 3.5
86 1 1 0 10.0431 5.79837 5.85461
87 1 1 0 11.4777 6.62669 8.20922
88 1 1 0 10.0431 7.45502 3.5
89 1 1 0 11.4777 8.28337 5.85461
90 1 1 0 12.9124 9.11167 8.20922
91 1 1 0 5.73888 -4.97002 3.5
92 1 1 0 7.1736 -4.14166 5.85461
93 1 1 0 8.60832 -3.31334 8.20922
94 1 1 0 7.1736 -2.48501 3.5
95 1 1 0 8.60832 -1.65666 5.85461
96 1 1 0 10.0431 -0.828336 8.20922
97 1 1 0 8.60832 0 3.5
98 1 1 0 10.0431 0.828352 5.85461
99 1 1 0 11.4777 1.65667 8.20922
100 1 1 0 10.0431 2.48501 3.5
101 1 1 0 11.4777 3.31336 5.85461
102 1 1 0 12.9124 4.14168 8.20922
103 1 1 0 11.4777 4.97002 3.5
104 1 1 0 12.9124 5.79837 5.85461
105 1 1 0 14.3472 6.62669 8.20922
106 1 1 0 12.9124 7.45502 3.5
107 1 1 0 14.3472 8.28337 5.85461
108 1 1 0 15.7819 9.11167 8.20922
109 2 2 0 -11.0678 -6.39002 0
110 2 2 0 -9.83808 -5.68001 0
111 2 2 0 -9.83808 -4.26001 0
112 2 2 0 -8.60832 -3.55001 0
113 2 2 0 -8.60832 -2.13001 0
114 2 2 0 -7.37856 -1.42 0
115 2 2 0 -7.37856 0 0
116 2 2 0 -6.1488 0.710007 0
117 2 2 0 -6.1488 2.13001 0
118 2 2 0 -4.91904 2.84001 0
119 2 2 0 -4.91904 4.26001 0
120 2 2 0 -3.68928 4.97002 0
121 2 2 0 -3.68928 6.39002 0
122 2 2 0 -2.45952 7.10003 0
123 2 2 0 -8.60832 -6.39002 0
124 2 2 0 -7.37856 -5.68001 0
125 2 2 0 -7.37856 -4.26001 0
126 2 2 0 -6.1488 -3.55001 0
127 2 2 0 -6.1488 -2.13001 0
128 2 2 0 -4.91904 -1.42 0
129 2 2 0 -4.91904 0 0
130 2 2 0 -3.68928 0.710007 0
131 2 2 0 -3.68928 2.13001 0
132 2 2 0 -2.45952 2.84001 0
133 2 2 0 -2.45952 4.26001 0
134 2 2 0 -1.22976 4.97002 0
135 2 2 0 -1.22976 6.39002 0
136 2 2 0 0 7.10003 0
137 2 2 0 -6.1488 -6.39002 0
138 2 2 0 -4.91904 -5.68001 0
139 2 2 0 -4.91904 -4.26001 0
140 2 2 0 -3.68928 -3.55001 0
141 2 2 0 -3.68928 -2.13001 0
142 2 2 0 -2.45952 -1.42 0
143 2 2 0 -2.45952 0 0
144 2 2 0 -1.22976 0.710007 0
145 2 2 0 -1.22976 2.13001 0
146 2 2 0 0 2.84001 0
147 2 2 0 0 4.26001 0
148 2 2 0 1.22976 4.97002 0
149 2 2 0 1.22976 6.39002 0
150 2 2 0 2.45952 7.10003 0
151 2 2 0 -3.68928 -6.39002 0
152 2 2 0 -2.45952 -5.68001 0
153 2 2 0 -2.45952 -4.26001 0
154 2 2 0 -1.22976 -3.55001 0
155 2 2 0 -1.22976 -2.13001 0
156 2 2 0 0 -1.42 0
157 2 2 0 0 0 0
158 2 2 0 1.22976 0.710007 0
159 2 2 0 1.22976 2.13001 0
160 2 2 0 2.45952 2.84001 0
161 2 2 0 2.45952 4.26001 0
162 2 2 0 3.68928 4.97002 0
163 2 2 0 3.68928 6.39002 0
164 2 2 0 4.91904 7.10003 0
165 2 2 0 -1.22976 -6.39002 0
166 2 2 0 0 -5.68001 0
167 2 2 0 0 -4.26001 0
168 2 2 0 1.22976 -3.55001 0
169 2 2 0 1.22976 -2.13001 0
170 2 2 0 2.45952 -1.42 0
171 2 2 0 2.45952 0 0
172 2 2 0 3.68928 0.710007 0
173 2 2 0 3.68928 2.13001 0
174 2 2 0 4.91904 2.84001 0
175 2 2 0 4.91904 4.26001 0
176 2 2 0 6.1488 4.97002 0
177 2 2 0 6.1488 6.39002 0
178 2 2 0 7.37856 7.10003 0
179 2 2 0 1.22976 -6.39002 0
180 2 2 0 2.45952 -5.68001 0
181 2 2 0 2.45952 -4.26001 0
182 2 2 0 3.68928 -3.55001 0
183 2 2 0 3.68928 -2.13001 0
184 2 2 0 4.91904 -1.42 0
185 2 2 0 4.91904 0 0
186 2 2 0 6.1488 0.710007 0
187 2 2 0 6.1488 2.13001 0
188 2 2 0 7.37856 2.84001 0
189 2 2 0 7.37856 4.26001 0
190 2 2 0 8.60832 4.97002 0
191 2 2 0 8.60832 6.39002 0
192 2 2 0 9.83808 7.10003 0
193 2 2 0 3.68928 -6.39002 0
194 2 2 0 4.91904 -5.68001 0
195 2 2 0 4.91904 -4.26001 0
196 2 2 0 6.1488 -3.55001 0
197 2 2 0 6.1488 -2.13001 0
198 2 2 0 7.37856 -1.42 0
199 2 2 0 7.37856 0 0
200 2 2 0 8.60832 0.710007 0
201 2 2 0 8.60832 2.13001 0
202 2 2 0 9.83808 2.84001 0
203 2 2 0 9.83808 4.26001 0
204 2 2 0 11.0678 4.97002 0
205 2 2 0 11.0678 6.39002 0
206 2 2 0 12.2976 7.10003 0

1
examples/PACKAGES/interlayer/saip_metal/Au_u3.eam Symbolic link
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../../../../potentials/Au_u3.eam

1
examples/PACKAGES/interlayer/saip_metal/CH.rebo Symbolic link
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../../../../potentials/CH.rebo

1
examples/PACKAGES/interlayer/saip_metal/CHAu.ILP Symbolic link
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../../../../potentials/CHAu.ILP

44
examples/PACKAGES/interlayer/saip_metal/in.gold_gr Normal file
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units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
# global group definition
group gold type 1
group gra type 2
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
pair_coeff * * rebo ./CH.rebo NULL C
pair_coeff * * saip/metal ./CHAu.ILP Au C
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000

164
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@ -0,0 +1,164 @@
LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
Reading data file ...
triclinic box = (0 0 -30) to (17.21664 14.910048 30) with tilt (8.60832 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
206 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
# global group definition
group gold type 1
108 atoms in group gold
group gra type 2
98 atoms in group gra
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
Reading eam potential file ./Au_u3.eam with DATE: 2007-06-11
pair_coeff * * rebo ./CH.rebo NULL C
Reading rebo potential file ./CH.rebo with DATE: 2018-7-3
pair_coeff * * saip/metal ./CHAu.ILP Au C
Reading saip/metal potential file ./CHAu.ILP with DATE: 2021-12-02
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- saip/metal potential doi.org/10.1021/acs.jctc.1c00622
@Article{Ouyang2021
author = {W. Ouyang, O. Hod, and R. Guerra},
title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7215-7223}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 3 2 7
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair eam, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(3) pair saip/metal, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.747 | 9.747 | 9.747 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp
0 -1121.4621 -1129.3728 7.9107209 -724.70925 -6.0302289 298.53659
100 -1121.4483 -1124.9731 3.5248501 -723.03272 -5.9765533 133.02159
200 -1121.4403 -1125.2912 3.8509646 -722.66784 -6.0468507 145.32858
300 -1121.4424 -1126.4665 5.0240531 -722.72787 -6.0350568 189.59886
400 -1121.4419 -1125.1443 3.7023978 -722.59976 -5.8294548 139.72193
500 -1121.4413 -1125.2711 3.8297939 -722.5342 -6.0189944 144.52963
600 -1121.4449 -1125.8808 4.4359049 -722.77707 -5.8685221 167.40319
700 -1121.4489 -1126.1966 4.747709 -723.13681 -5.8666379 179.17012
800 -1121.4443 -1125.8469 4.402607 -722.94487 -6.0094567 166.14658
900 -1121.4424 -1125.8437 4.4013317 -722.94918 -5.8699702 166.09846
1000 -1121.4467 -1125.7453 4.2986881 -722.66682 -6.0651168 162.22487
Loop time of 6.43246 on 1 procs for 1000 steps with 206 atoms
Performance: 13.432 ns/day, 1.787 hours/ns, 155.462 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.4201 | 6.4201 | 6.4201 | 0.0 | 99.81
Bond | 8.9059e-05 | 8.9059e-05 | 8.9059e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0071852 | 0.0071852 | 0.0071852 | 0.0 | 0.11
Output | 0.00026031 | 0.00026031 | 0.00026031 | 0.0 | 0.00
Modify | 0.0019433 | 0.0019433 | 0.0019433 | 0.0 | 0.03
Other | | 0.002875 | | | 0.04
Nlocal: 206 ave 206 max 206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2187 ave 2187 max 2187 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 158548 ave 158548 max 158548 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158548
Ave neighs/atom = 769.65049
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

164
examples/PACKAGES/interlayer/saip_metal/log.7Jan22.gold_gr.g++.4 Normal file
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@ -0,0 +1,164 @@
LAMMPS (7 Jan 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
processors * * 1
boundary p p f
read_data ./3Lgold_1Lgr_atop_sliding.data
Reading data file ...
triclinic box = (0 0 -30) to (17.21664 14.910048 30) with tilt (8.60832 0 0)
2 by 2 by 1 MPI processor grid
reading atoms ...
206 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# global group definition
group gold type 1
108 atoms in group gold
group gra type 2
98 atoms in group gra
# Define mass
mass * 12.0107 # mass of carbon atom , uint: a.u.=1.66X10^(-27)kg
mass 1 196.96657 # mass of gold atom , uint: a.u.=1.66X10^(-27)kg
# Define potentials
pair_style hybrid/overlay eam rebo saip/metal 16.0
pair_coeff 1 1 eam ./Au_u3.eam
Reading eam potential file ./Au_u3.eam with DATE: 2007-06-11
pair_coeff * * rebo ./CH.rebo NULL C
Reading rebo potential file ./CH.rebo with DATE: 2018-7-3
pair_coeff * * saip/metal ./CHAu.ILP Au C
Reading saip/metal potential file ./CHAu.ILP with DATE: 2021-12-02
# compute energy
compute 0 all pair rebo
compute 1 all pair eam
compute 2 all pair saip/metal
variable REBO equal c_0
variable EAM equal c_1
variable ILP equal c_2
thermo_style custom step etotal pe ke v_REBO v_ILP temp
thermo 100
thermo_modify lost error
# Creat initial velocity
velocity all set 0.0 0.0 0.0
velocity gra create 300.0 4928459 mom yes rot yes dist gaussian
velocity gold create 300.0 4928459 mom yes rot yes dist gaussian
# Integration
fix intsub gold nve
fix intrib gra nve
timestep 1e-3
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = {6009}
year = 2018,
}
- saip/metal potential doi.org/10.1021/acs.jctc.1c00622
@Article{Ouyang2021
author = {W. Ouyang, O. Hod, and R. Guerra},
title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},
journal = {J. Chem. Theory Comput.},
volume = 17,
pages = {7215-7223}
year = 2021,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 3 2 7
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair eam, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(3) pair saip/metal, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.299 | 9.299 | 9.3 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp
0 -1121.4621 -1129.3728 7.9107209 -724.70925 -6.0302289 298.53659
100 -1121.4483 -1124.9731 3.5248501 -723.03272 -5.9765533 133.02159
200 -1121.4403 -1125.2912 3.8509646 -722.66784 -6.0468507 145.32858
300 -1121.4424 -1126.4665 5.0240531 -722.72787 -6.0350568 189.59886
400 -1121.4419 -1125.1443 3.7023978 -722.59976 -5.8294548 139.72193
500 -1121.4413 -1125.2711 3.8297939 -722.5342 -6.0189944 144.52963
600 -1121.4449 -1125.8808 4.4359049 -722.77707 -5.8685221 167.40319
700 -1121.4489 -1126.1966 4.747709 -723.13681 -5.8666379 179.17012
800 -1121.4443 -1125.8469 4.402607 -722.94487 -6.0094567 166.14658
900 -1121.4424 -1125.8437 4.4013317 -722.94918 -5.8699702 166.09846
1000 -1121.4467 -1125.7453 4.2986881 -722.66682 -6.0651168 162.22487
Loop time of 2.44776 on 4 procs for 1000 steps with 206 atoms
Performance: 35.298 ns/day, 0.680 hours/ns, 408.537 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6906 | 2.0172 | 2.3939 | 19.2 | 82.41
Bond | 5.4278e-05 | 6.3818e-05 | 7.3153e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.049363 | 0.42514 | 0.75161 | 41.7 | 17.37
Output | 0.00018596 | 0.00020656 | 0.00024754 | 0.0 | 0.01
Modify | 0.00063656 | 0.00074701 | 0.00089514 | 0.0 | 0.03
Other | | 0.004362 | | | 0.18
Nlocal: 51.5 ave 61 max 44 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1670.75 ave 1699 max 1641 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 39637 ave 47080 max 33737 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 158548
Ave neighs/atom = 769.65049
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

2
examples/README
View File

@ -94,7 +94,7 @@ msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
numdiff: numerical difference computation of forces
numdiff: numerical difference computation of forces and virial
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter

87
examples/numdiff/in.numdiff
View File

@ -1,33 +1,74 @@
# Numerical difference calculation of error in forces
# Numerical difference calculation
# of error in forces and virial stress
units metal
atom_style atomic
# adjustable parameters
atom_modify map yes
lattice fcc 5.358000
region box block 0 6 0 6 0 6
create_box 1 box
create_atoms 1 box
mass 1 39.903
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
velocity all create 10 2357 mom yes dist gaussian
units metal
atom_style atomic
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
atom_modify map yes
lattice fcc 5.358000
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
create_box 1 box
create_atoms 1 box
mass 1 39.903
neighbor 1 bin
velocity all create ${temp} 2357 mom yes dist gaussian
timestep 0.001
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
fix numdiff all numdiff 200 0.0001
fix nve all nve
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
variable errx atom fx-f_numdiff[1]
variable erry atom fy-f_numdiff[2]
variable errz atom fz-f_numdiff[3]
timestep 0.001
fix nve all nve
write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]
# define numerical force calculation
dump forces all custom 200 force_error.dump v_errx v_erry v_errz
thermo 200
run 2000
fix numforce all numdiff ${nthermo} ${fdelta}
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + &
v_erryy^2 + &
v_errzz^2 + &
v_erryz^2 + &
v_errxz^2 + &
v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + &
c_myvirial[3]^2 + &
c_myvirial[3]^2 + &
c_myvirial[4]^2 + &
c_myvirial[5]^2 + &
c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
run ${nsteps}

175
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@ -0,0 +1,175 @@
LAMMPS (7 Jan 2022)
# Numerical difference calculation
# of error in forces and virial stress
# adjustable parameters
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
units metal
atom_style atomic
atom_modify map yes
lattice fcc 5.358000
Lattice spacing in x,y,z = 5.358 5.358 5.358
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
region box block 0 3 0 ${nlat} 0 ${nlat}
region box block 0 3 0 3 0 ${nlat}
region box block 0 3 0 3 0 3
create_box 1 box
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
create_atoms CPU = 0.000 seconds
mass 1 39.903
velocity all create ${temp} 2357 mom yes dist gaussian
velocity all create 10.0 2357 mom yes dist gaussian
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
timestep 0.001
fix nve all nve
# define numerical force calculation
fix numforce all numdiff ${nthermo} ${fdelta}
fix numforce all numdiff 10 ${fdelta}
fix numforce all numdiff 10 1.0e-4
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
fix numvirial all numdiff/virial 10 ${vdelta}
fix numvirial all numdiff/virial 10 1.0e-6
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
thermo 10
run ${nsteps}
run 500
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.9407173
ghost atom cutoff = 5.9407173
binsize = 2.9703587, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06
10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07
20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06
30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07
40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08
50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08
60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08
70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08
80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08
90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08
100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08
110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08
120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08
130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08
140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09
150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09
160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09
170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08
180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09
190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09
200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08
210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08
220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09
230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08
240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08
250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08
260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09
270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08
280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08
290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08
300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08
310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08
320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08
330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08
340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08
350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08
360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08
370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08
380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08
390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08
400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08
410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08
420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08
430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08
440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08
450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08
460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08
470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08
480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08
490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08
500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08
Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms
Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17
Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70
Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66
Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51
Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89
Other | | 0.0006258 | | | 0.07
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 558 ave 558 max 558 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 972 ave 972 max 972 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 972
Ave neighs/atom = 9
Neighbor list builds = 500
Dangerous builds not checked
Total wall time: 0:00:00

175
examples/numdiff/log.28Jan2022.log.numdiff.g++.4 Normal file
View File

@ -0,0 +1,175 @@
LAMMPS (7 Jan 2022)
# Numerical difference calculation
# of error in forces and virial stress
# adjustable parameters
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
units metal
atom_style atomic
atom_modify map yes
lattice fcc 5.358000
Lattice spacing in x,y,z = 5.358 5.358 5.358
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
region box block 0 3 0 ${nlat} 0 ${nlat}
region box block 0 3 0 3 0 ${nlat}
region box block 0 3 0 3 0 3
create_box 1 box
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
create_atoms CPU = 0.000 seconds
mass 1 39.903
velocity all create ${temp} 2357 mom yes dist gaussian
velocity all create 10.0 2357 mom yes dist gaussian
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
timestep 0.001
fix nve all nve
# define numerical force calculation
fix numforce all numdiff ${nthermo} ${fdelta}
fix numforce all numdiff 10 ${fdelta}
fix numforce all numdiff 10 1.0e-4
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
fix numvirial all numdiff/virial 10 ${vdelta}
fix numvirial all numdiff/virial 10 1.0e-6
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
thermo 10
run ${nsteps}
run 500
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.9407173
ghost atom cutoff = 5.9407173
binsize = 2.9703587, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
0 10 -7.0259569 -6.8876486 28.564278 10664.391 9.1481187e-08
10 9.9388179 -7.0251107 -6.8876486 30.21736 1.4771865e-08 1.3452512e-07
20 9.7572185 -7.022599 -6.8876485 35.123527 1.437525e-08 8.0966999e-07
30 9.4606673 -7.0184974 -6.8876484 43.132052 1.4375468e-08 1.990012e-08
40 9.0579092 -7.0129268 -6.8876483 54.000927 1.4350331e-08 1.7239028e-08
50 8.5607685 -7.0060508 -6.8876482 67.403151 1.4353284e-08 7.813181e-09
60 7.9838726 -6.9980717 -6.8876481 82.935358 1.4398078e-08 2.022316e-08
70 7.3442875 -6.9892255 -6.8876479 100.12892 1.434409e-08 7.5938179e-09
80 6.6610579 -6.9797757 -6.8876477 118.46358 1.4324787e-08 7.1972571e-09
90 5.9546462 -6.9700053 -6.8876476 137.38365 1.4322718e-08 4.3978378e-09
100 5.2462727 -6.9602077 -6.8876474 156.31651 1.4273172e-08 4.6728038e-09
110 4.5571706 -6.9506767 -6.8876472 174.69294 1.4266163e-08 3.522225e-09
120 3.9077807 -6.9416949 -6.887647 191.96859 1.42241e-08 3.5357511e-09
130 3.3169241 -6.9335227 -6.8876469 207.64566 1.4203813e-08 2.5182488e-09
140 2.8010028 -6.926387 -6.8876468 221.29333 1.4164215e-08 2.3112509e-09
150 2.3732854 -6.9204712 -6.8876467 232.5658 1.4134122e-08 1.9368963e-09
160 2.0433329 -6.9159076 -6.8876466 241.21647 1.4095473e-08 3.6806452e-09
170 1.8166184 -6.912772 -6.8876466 247.10715 1.4049531e-08 2.5319322e-09
180 1.6943727 -6.9110813 -6.8876467 250.21143 1.3997912e-08 1.952404e-09
190 1.6736731 -6.910795 -6.8876467 250.61203 1.3915487e-08 1.4271767e-09
200 1.7477659 -6.9118199 -6.8876468 248.49223 1.3850618e-08 2.4515718e-09
210 1.9065921 -6.9140167 -6.8876469 244.12226 1.3747916e-08 1.7957531e-09
220 2.1374676 -6.91721 -6.887647 237.84173 1.3674779e-08 2.6613511e-09
230 2.4258607 -6.9211989 -6.8876472 230.0395 1.3565712e-08 3.0777067e-09
240 2.7562034 -6.9257679 -6.8876473 221.13265 1.3440442e-08 1.7111501e-09
250 3.1126827 -6.9306984 -6.8876474 211.54566 1.3270914e-08 1.6690112e-09
260 3.4799641 -6.9357784 -6.8876476 201.69126 1.3105092e-08 2.1637558e-09
270 3.8438148 -6.9408108 -6.8876477 191.95361 1.2962846e-08 4.4613506e-09
280 4.191607 -6.9456212 -6.8876478 182.6745 1.2846383e-08 3.3730203e-09
290 4.5126922 -6.9500621 -6.8876478 174.14285 1.2710692e-08 2.2809889e-09
300 4.7986487 -6.9540172 -6.8876479 166.58747 1.2657778e-08 6.9880891e-09
310 5.0434083 -6.9574025 -6.8876479 160.17316 1.266381e-08 4.2486217e-09
320 5.243275 -6.9601668 -6.8876479 154.99974 1.279856e-08 5.1505673e-09
330 5.3968455 -6.9622908 -6.8876479 151.1038 1.2981831e-08 3.3339333e-09
340 5.5048468 -6.9637845 -6.8876479 148.46296 1.3159021e-08 1.7881393e-09
350 5.569902 -6.9646843 -6.8876479 147.00205 1.3439465e-08 5.6876219e-09
360 5.5962378 -6.9650485 -6.8876478 146.60113 1.3645943e-08 7.233847e-09
370 5.5893468 -6.9649531 -6.8876478 147.10471 1.3829581e-08 4.5514318e-09
380 5.5556199 -6.9644866 -6.8876477 148.33195 1.4005893e-08 4.2971846e-09
390 5.5019639 -6.9637444 -6.8876476 150.08725 1.4157454e-08 3.3564262e-09
400 5.4354239 -6.962824 -6.8876476 152.17073 1.4226422e-08 4.2393923e-09
410 5.3628267 -6.9618199 -6.8876475 154.38825 1.4302679e-08 3.8937698e-09
420 5.2904639 -6.960819 -6.8876475 156.56034 1.4381099e-08 4.315875e-09
430 5.2238282 -6.9598973 -6.8876474 158.52969 1.4426567e-08 4.2658185e-09
440 5.1674149 -6.9591171 -6.8876474 160.16704 1.4453381e-08 5.7055268e-09
450 5.1245913 -6.9585248 -6.8876474 161.37513 1.4449488e-08 4.4308801e-09
460 5.0975361 -6.9581506 -6.8876474 162.09077 1.4445596e-08 5.8269923e-09
470 5.0872416 -6.9580082 -6.8876474 162.28517 1.4444348e-08 4.8263194e-09
480 5.0935712 -6.9580957 -6.8876474 161.96268 1.4411666e-08 6.222228e-09
490 5.115362 -6.9583971 -6.8876474 161.15816 1.4369716e-08 3.3926077e-09
500 5.1505605 -6.958884 -6.8876474 159.9333 1.4288515e-08 3.8845251e-09
Loop time of 0.252598 on 4 procs for 500 steps with 108 atoms
Performance: 171.023 ns/day, 0.140 hours/ns, 1979.430 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021545 | 0.0022845 | 0.0023794 | 0.2 | 0.90
Neigh | 0.0063887 | 0.0067604 | 0.0069752 | 0.3 | 2.68
Comm | 0.01048 | 0.010916 | 0.011408 | 0.3 | 4.32
Output | 0.0026603 | 0.0027399 | 0.0029738 | 0.3 | 1.08
Modify | 0.2295 | 0.22952 | 0.22954 | 0.0 | 90.86
Other | | 0.0003814 | | | 0.15
Nlocal: 27 ave 29 max 25 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 325 ave 327 max 323 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 243 ave 273 max 228 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 972
Ave neighs/atom = 9
Neighbor list builds = 500
Dangerous builds not checked
Total wall time: 0:00:00

18
examples/plugins/angle_zero2.h
View File

@ -21,17 +21,17 @@ namespace LAMMPS_NS {
class AngleZero2 : public Angle {
public:
AngleZero2(class LAMMPS *);
virtual ~AngleZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~AngleZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
double equilibrium_angle(int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int);
double single(int, int, int, int) override;
protected:
double *theta0;

20
examples/plugins/bond_zero2.h
View File

@ -21,18 +21,18 @@ namespace LAMMPS_NS {
class BondZero2 : public Bond {
public:
BondZero2(class LAMMPS *);
virtual ~BondZero2();
virtual void compute(int, int);
virtual void settings(int, char **);
~BondZero2() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void coeff(int, char **) override;
double equilibrium_distance(int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, double, int, int, double &);
virtual void *extract(const char *, int &);
double single(int, double, int, int, double &) override;
void *extract(const char *, int &) override;
protected:
double *r0;

14
examples/plugins/dihedral_zero2.h
View File

@ -25,14 +25,14 @@ namespace LAMMPS_NS {
class DihedralZero2 : public Dihedral {
public:
DihedralZero2(class LAMMPS *);
virtual ~DihedralZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~DihedralZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
protected:
int coeffflag;

23
examples/plugins/fix_nve2.h
View File

@ -11,12 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(nve2, FixNVE2)
#else
#ifndef LMP_FIX_NVE2_H
#define LMP_FIX_NVE2_H
@ -27,14 +21,14 @@ namespace LAMMPS_NS {
class FixNVE2 : public Fix {
public:
FixNVE2(class LAMMPS *, int, char **);
virtual ~FixNVE2() {}
int setmask();
virtual void init();
virtual void initial_integrate(int);
virtual void final_integrate();
virtual void initial_integrate_respa(int, int, int);
virtual void final_integrate_respa(int, int);
virtual void reset_dt();
int setmask() override;
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
void initial_integrate_respa(int, int, int) override;
void final_integrate_respa(int, int) override;
void reset_dt() override;
protected:
double dtv, dtf;
@ -44,7 +38,6 @@ class FixNVE2 : public Fix {
} // namespace LAMMPS_NS
#endif
#endif
/* ERROR/WARNING messages:

14
examples/plugins/improper_zero2.h
View File

@ -21,14 +21,14 @@ namespace LAMMPS_NS {
class ImproperZero2 : public Improper {
public:
ImproperZero2(class LAMMPS *);
virtual ~ImproperZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~ImproperZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
protected:
int coeffflag;

26
examples/plugins/pair_morse2.h
View File

@ -21,20 +21,20 @@ namespace LAMMPS_NS {
class PairMorse2 : public Pair {
public:
PairMorse2(class LAMMPS *);
virtual ~PairMorse2();
virtual void compute(int, int);
~PairMorse2() override;
void compute(int, int) override;
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
void settings(int, char **) override;
void coeff(int, char **) override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
void *extract(const char *, int &) override;
protected:
double cut_global;

4
examples/plugins/pair_morse2_omp.h
View File

@ -28,8 +28,8 @@ class PairMorse2OMP : public PairMorse2, public ThrOMP {
public:
PairMorse2OMP(class LAMMPS *);
virtual void compute(int, int);
virtual double memory_usage();
void compute(int, int) override;
double memory_usage() override;
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>

26
examples/plugins/pair_zero2.h
View File

@ -31,19 +31,19 @@ namespace LAMMPS_NS {
class PairZero2 : public Pair {
public:
PairZero2(class LAMMPS *);
virtual ~PairZero2();
virtual void compute(int, int);
virtual void compute_outer(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
~PairZero2() override;
void compute(int, int) override;
void compute_outer(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
protected:
double cut_global;

2
lib/gpu/lal_answer.cpp
View File

@ -248,7 +248,7 @@ double AnswerT::energy_virial(double *eatom, double **vatom,
return energy_virial(eatom,vatom,virial);
double evdwl=0.0;
int ii, vstart=0, iend=_ev_stride;
int vstart=0, iend=_ev_stride;
if (_eflag) {
iend=_ev_stride*2;
#if (LAL_USE_OMP_SIMD == 1)

16
lib/gpu/lal_base_atomic.cpp
View File

@ -239,14 +239,14 @@ void BaseAtomicT::compute(const int f_ago, const int inum_full,
// Reneighbor on GPU if necessary and then compute forces, virials, energies
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int ** BaseAtomicT::compute(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special,
const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success) {
int **BaseAtomicT::compute(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special,
const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;

12
lib/gpu/lal_base_atomic.h
View File

@ -133,20 +133,12 @@ class BaseAtomic {
int &host_start, const double cpu_time, bool &success);
/// Pair loop with device neighboring
int * compute(const int ago, const int inum_full,
int **compute(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
/// Pair loop with device neighboring
int ** compute(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **numj, const double cpu_time, bool &success);
int **ilist, int **numj, const double cpu_time, bool &success);
// -------------------------- DEVICE DATA -------------------------

2
lib/gpu/lal_base_ellipsoid.cpp
View File

@ -69,7 +69,7 @@ BaseEllipsoidT::~BaseEllipsoid() {
}
template <class numtyp, class acctyp>
int BaseEllipsoidT::bytes_per_atom(const int max_nbors) const {
int BaseEllipsoidT::bytes_per_atom_ellipsoid(const int max_nbors) const {
return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
nbor->bytes_per_atom(max_nbors);
}

21
lib/gpu/lal_base_ellipsoid.h
View File

@ -108,7 +108,7 @@ class BaseEllipsoid {
void output_times();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
int bytes_per_atom_ellipsoid(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage_base() const;
@ -173,18 +173,13 @@ class BaseEllipsoid {
const double cpu_time, bool &success, double **quat);
/// Pair loop with device neighboring
int** compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **numj, const double cpu_time, bool &success,
double **host_quat);
/// Build neighbor list on accelerator
void build_nbor_list(const int inum, const int host_inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, bool &success);
int**compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **numj, const double cpu_time, bool &success,
double **host_quat);
// -------------------------- DEVICE DATA -------------------------

2
lib/gpu/lal_device.cpp
View File

@ -198,7 +198,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu,
// Find deviceID with most CUs (priority given to the accelerator type)
if (_first_device < 0) {
int best_device = 0;
int best_cus = gpu->cus(0);
unsigned best_cus = gpu->cus(0);
bool type_match = (gpu->device_type(0) == type);
for (int i = 1; i < gpu->num_devices(); i++) {
if (type_match==true && gpu->device_type(i)!=type)

3
lib/gpu/lal_eam.h
View File

@ -62,9 +62,6 @@ class EAM : public BaseAtomic<numtyp, acctyp> {
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;

2
lib/gpu/lal_gayberne.cpp
View File

@ -43,7 +43,7 @@ GayBerneT::~GayBerne() {
template <class numtyp, class acctyp>
int GayBerneT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom(max_nbors);
return this->bytes_per_atom_ellipsoid(max_nbors);
}
template <class numtyp, class acctyp>

2
lib/gpu/lal_re_squared.cpp
View File

@ -43,7 +43,7 @@ RESquaredT::~RESquared() {
template <class numtyp, class acctyp>
int RESquaredT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom(max_nbors);
return this->bytes_per_atom_ellipsoid(max_nbors);
}
template <class numtyp, class acctyp>

14
lib/gpu/lal_sw.cu
View File

@ -658,6 +658,7 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_,
#ifndef ONETYPE
const int ktype=kx.w;
const int mtypek=jtype*ntypes+ktype;
const numtyp sw_cut_ik=cut_sig_gamma[mtypek].x;
#endif
numtyp delr2x = kx.x - jx.x;
@ -665,8 +666,12 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_,
numtyp delr2z = kx.z - jx.z;
numtyp rsq2 = delr2x*delr2x + delr2y*delr2y + delr2z*delr2z;
// for neigh no within pair hybrid: still need the check below
// this loop apparently iterates over neighbors of j that are not intended
const numtyp cutsq_jk=sw_cut_ik*sw_cut_ik;
if (!(rsq2>(numtyp)0 && rsq2<cutsq_jk)) continue;
#ifndef ONETYPE
const numtyp sw_cut_ik=cut_sig_gamma[mtypek].x;
const numtyp sw_sigma_gamma_ik=cut_sig_gamma[mtypek].y;
const int mtypejik=jtype*ntypes*ntypes+itype+ktype;
const numtyp sw_lambda_epsilon_ijk=sw_pre3[mtypejik].x;
@ -775,6 +780,7 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_,
#ifndef ONETYPE
const int ktype=kx.w;
const int mtypek=jtype*ntypes+ktype;
const numtyp sw_cut_ik=cut_sig_gamma[mtypek].x;
#endif
numtyp delr2x = kx.x - jx.x;
@ -782,8 +788,12 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_,
numtyp delr2z = kx.z - jx.z;
numtyp rsq2 = delr2x*delr2x + delr2y*delr2y + delr2z*delr2z;
// for neigh no within pair hybrid: still need the check below
// this loop apparently iterates over neighbors of j that are not intended
const numtyp cutsq_jk=sw_cut_ik*sw_cut_ik;
if (!(rsq2>(numtyp)0 && rsq2<cutsq_jk)) continue;
#ifndef ONETYPE
const numtyp sw_cut_ik=cut_sig_gamma[mtypek].x;
const numtyp sw_sigma_gamma_ik=cut_sig_gamma[mtypek].y;
const int mtypejik=jtype*ntypes*ntypes+itype+ktype;
const numtyp sw_lambda_epsilon_ijk=sw_pre3[mtypejik].x;

3
lib/kokkos/Makefile.kokkos
View File

@ -1224,6 +1224,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp)
ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1)
KOKKOS_SRC += $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_HIP.cpp
endif
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.hpp)
KOKKOS_CXXFLAGS+=$(KOKKOS_INTERNAL_HIP_ARCH_FLAG)

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