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lammps
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Merge branch 'master' into kk_binsize

This commit is contained in:
Stan Moore 2019-04-08 12:07:58 -06:00
parent 0d73fe99fd 898860328b
commit aa336c2bb4
844 changed files with 18209 additions and 9470 deletions
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398
cmake/CMakeLists.txt
View File

@ -320,10 +320,15 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
pkg_depends(USER-SCAFACOS MPI)
include(CheckIncludeFileCXX)
find_package(OpenMP QUIET)
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find required 'omp.h' header file")
endif()
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
@ -367,7 +372,7 @@ if(PKG_KSPACE)
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@ -381,19 +386,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
endif()
if(PKG_PYTHON)
find_package(PythonInterp REQUIRED)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
include_directories(${PYTHON_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
if(BUILD_LIB AND BUILD_SHARED_LIBS)
if(NOT PYTHON_INSTDIR)
execute_process(COMMAND ${PYTHON_EXECUTABLE}
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
endif()
endif()
find_package(JPEG QUIET)
@ -452,7 +448,13 @@ endif()
if(PKG_VORONOI)
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
find_package(VORO)
if(VORO_FOUND)
set(DOWNLOAD_VORO_DEFAULT OFF)
else()
set(DOWNLOAD_VORO_DEFAULT ON)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
@ -485,7 +487,13 @@ if(PKG_VORONOI)
endif()
if(PKG_LATTE)
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
find_package(LATTE)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
set(DOWNLOAD_LATTE_DEFAULT ON)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
@ -496,7 +504,7 @@ if(PKG_LATTE)
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
URL_MD5 85ac414fdada2d04619c8f936344df14
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
@ -512,7 +520,15 @@ endif()
if(PKG_USER-SCAFACOS)
find_package(GSL REQUIRED)
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
find_package(PkgConfig QUIET)
set(DOWNLOAD_SCAFACOS_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(SCAFACOS QUIET scafacos)
if(SCAFACOS_FOUND)
set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own")
include(ExternalProject)
@ -552,8 +568,8 @@ if(PKG_USER-SCAFACOS)
list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
else()
FIND_PACKAGE(PkgConfig REQUIRED)
PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED scafacos)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
endif()
include_directories(${SCAFACOS_INCLUDE_DIRS})
@ -567,29 +583,53 @@ if(PKG_USER-PLUMED)
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
URL_MD5 71ed465bdc7c2059e282dbda8d564e71
URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
URL_MD5 c2a7b519e32197a120cdf47e0f194f81
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
--enable-modules=all
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
list(APPEND LAMMPS_DEPS plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
"${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "SHARED")
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "RUNTIME")
add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
@ -597,7 +637,7 @@ if(PKG_USER-PLUMED)
set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED plumed REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
@ -613,9 +653,13 @@ if(PKG_USER-PLUMED)
endif()
if(PKG_USER-MOLFILE)
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
list(APPEND LAMMPS_LINK_LIBS molfile)
endif()
@ -626,9 +670,14 @@ if(PKG_USER-NETCDF)
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
if(PKG_USER-SMD)
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
find_package(Eigen3 NO_MODULE)
if(EIGEN3_FOUND)
set(DOWNLOAD_EIGEN3_DEFAULT OFF)
else()
set(DOWNLOAD_EIGEN3_DEFAULT ON)
endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
@ -670,15 +719,27 @@ if(PKG_USER-VTK)
endif()
if(PKG_KIM)
option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
find_package(CURL)
if(CURL_FOUND)
include_directories(${CURL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
add_definitions(-DLMP_KIM_CURL)
endif()
find_package(KIM-API QUIET)
if(KIM-API_FOUND)
set(DOWNLOAD_KIM_DEFAULT OFF)
else()
set(DOWNLOAD_KIM_DEFAULT ON)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
message(STATUS "KIM-API v2 download requested - we will build our own")
message(STATUS "KIM-API download requested - we will build our own")
enable_language(C)
enable_language(Fortran)
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
URL_MD5 537d9c0abd30f85b875ebb584f9143fa
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@ -687,17 +748,14 @@ if(PKG_KIM)
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM-API-V2)
if(NOT KIM-API-V2_FOUND)
message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
endif()
find_package(KIM-API REQUIRED)
endif()
list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
include_directories(${KIM-API-V2_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
include_directories(${KIM-API_INCLUDE_DIRS})
endif()
if(PKG_MESSAGE)
@ -712,6 +770,7 @@ if(PKG_MESSAGE)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
@ -731,7 +790,13 @@ endif()
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@ -780,7 +845,6 @@ endif()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFileCXX)
foreach(HEADER cmath)
check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
@ -947,7 +1011,7 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
@ -1060,37 +1124,79 @@ if(PKG_OPT)
endif()
if(PKG_USER-INTEL)
find_package(TBB REQUIRED)
find_package(MKL REQUIRED)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG")
endif()
add_definitions(-DLMP_USER_INTEL)
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
endif()
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
if(NOT BUILD_OMP)
message(FATAL_ERROR "USER-INTEL requires OpenMP")
endif()
if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64")
message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64")
endif()
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
if(INTEL_ARCH STREQUAL "KNL")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
add_definitions(-DLMP_INTEL_OFFLOAD)
find_package(Threads QUIET)
if(Threads_FOUND)
set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
else()
set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
endif()
set(INTEL_LRT_VALUES none threads c++11)
set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
if(INTEL_LRT_MODE STREQUAL "THREADS")
if(Threads_FOUND)
add_definitions(-DLMP_INTEL_USELRT)
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
endif()
find_package(TBB QUIET)
if(TBB_FOUND)
list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
else()
add_definitions(-DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
find_package(MKL QUIET)
if(MKL_FOUND)
add_definitions(-DLMP_USE_MKL_RNG)
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
add_definitions(-DLMP_INTEL_OFFLOAD)
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
else()
@ -1103,33 +1209,33 @@ if(PKG_USER-INTEL)
add_compile_options(${_FLAG})
endif()
endforeach()
else()
add_compile_options(-O3 -ffast-math)
endif()
endif()
add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG)
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
${USER-INTEL_SOURCES_DIR}/intel_buffers.h
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
${USER-INTEL_SOURCES_DIR}/nbin_intel.h
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.h
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_simd.h
${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
# detects styles which have USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
include_directories(${USER-INTEL_SOURCES_DIR})
list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
include_directories(${USER-INTEL_SOURCES_DIR})
endif()
if(PKG_GPU)
@ -1171,6 +1277,10 @@ if(PKG_GPU)
message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
endif()
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
endif()
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
@ -1234,7 +1344,7 @@ if(PKG_GPU)
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
if(CUDPP_OPT)
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@ -1331,36 +1441,14 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
######################################
# Generate lmpgitversion.h
######################################
set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
set(temp_git_commit "(unknown)")
set(temp_git_branch "(unknown)")
set(temp_git_describe "(unknown)")
set(temp_git_info "false")
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
set(temp_git_info "true")
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
set(temp "${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}#endif\n\n")
message(STATUS "Generating lmpgitversion.h...")
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
-DGIT_FOUND="${GIT_FOUND}"
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
list(APPEND LAMMPS_DEPS gitversion)
###########################################
# Actually add executable and lib to build
@ -1406,9 +1494,19 @@ if(BUILD_EXE)
if(ENABLE_TESTING)
add_test(ShowHelp ${LAMMPS_BINARY} -help)
endif()
enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
target_link_libraries(msi2lmp m)
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif()
###############################################################################
# Build documentation
###############################################################################
@ -1470,11 +1568,14 @@ if(BUILD_DOC)
endif()
###############################################################################
# Install potential files in data directory
# Install potential and force field files in data directory
###############################################################################
set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
set(LAMMPS_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../tools/msi2lmp/frc_files/ DESTINATION ${LAMMPS_FRC_FILES_DIR})
configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
install(
@ -1483,6 +1584,49 @@ install(
DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
)
###############################################################################
# Install LAMMPS lib and python module into site-packages folder with
# "install-python" target. Behaves exactly like "make install-python" for
# conventional build. Only available, if a shared library is built.
# This is primarily for people that only want to use the Python wrapper.
###############################################################################
if(BUILD_LIB AND BUILD_SHARED_LIBS)
find_package(PythonInterp)
if (PYTHONINTERP_FOUND)
add_custom_target(
install-python
${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
-l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../python
COMMENT "Installing LAMMPS Python module")
else()
add_custom_target(
install-python
${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
endif()
else()
add_custom_target(
install-python
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
endif()
###############################################################################
# Add LAMMPS python module to "install" target. This is taylored for building
# LAMMPS for package managers and with different prefix settings.
# This requires either a shared library or that the PYTHON package is included.
###############################################################################
if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
find_package(PythonInterp)
if (PYTHONINTERP_FOUND)
execute_process(COMMAND ${PYTHON_EXECUTABLE}
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
endif()
endif()
###############################################################################
# Testing
#

33
cmake/Modules/FindKIM-API-V2.cmake → cmake/Modules/FindKIM-API.cmake
View File

@ -19,7 +19,7 @@
#
#
# Copyright (c) 2013--2018, Regents of the University of Minnesota.
# Copyright (c) 2013--2019, Regents of the University of Minnesota.
# All rights reserved.
#
# Contributors:
@ -28,23 +28,32 @@
# Ryan S. Elliott
#
# - Find KIM-API-V2
# - Find KIM-API
#
# sets standard pkg_check_modules variables plus:
#
# KIM-API-V2-CMAKE_C_COMPILER
# KIM-API-V2-CMAKE_CXX_COMPILER
# KIM-API-V2-CMAKE_Fortran_COMPILER
# KIM-API-CMAKE_C_COMPILER
# KIM-API-CMAKE_CXX_COMPILER
# KIM-API-CMAKE_Fortran_COMPILER
#
find_package(PkgConfig REQUIRED)
if(KIM-API_FIND_QUIETLY)
set(REQ_OR_QUI "QUIET")
else()
set(REQ_OR_QUI "REQUIRED")
endif()
find_package(PkgConfig ${REQ_OR_QUI})
include(FindPackageHandleStandardArgs)
pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
if(KIM-API_FOUND)
pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
endif()
# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE
# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)
find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

4
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -91,6 +91,10 @@ function(RegisterFixStyle path)
AddStyleHeader(${path} FIX)
endfunction(RegisterFixStyle)
function(RegisterIntegrateStyle path)
AddStyleHeader(${path} INTEGRATE)
endfunction(RegisterIntegrateStyle)
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid

30
cmake/Modules/generate_lmpgitversion.cmake Normal file
View File

@ -0,0 +1,30 @@
set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
set(temp_git_commit "(unknown)")
set(temp_git_branch "(unknown)")
set(temp_git_describe "(unknown)")
set(temp_git_info "false")
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
set(temp_git_info "true")
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
set(temp "${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}#endif\n\n")
message(STATUS "Generating lmpgitversion.h...")
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

31
cmake/README.md
View File

@ -155,11 +155,13 @@ make
The CMake build exposes a lot of different options. In the old build system
some of the package selections were possible by using special make target like
`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires
specifying all options manually. This can quickly become a very long command
line that is hard to handle. While these could be stored in a simple script
file, there is another way of defining "presets" to compile LAMMPS in a certain
way.
way. Since the cmake build process - contrary to the conventional build system -
includes the compilation of the bundled libraries into the standard build process,
the grouping of those presets is somewhat different.
A preset is a regular CMake script file that can use constructs such as
variables, lists and for-loops to manipulate configuration options and create
@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of
presets can be found in the `cmake/presets` folder.
```bash
# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package
mkdir build
cd build
cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake
```
# Reference
@ -1429,6 +1431,17 @@ TODO
</dl>
</td>
</tr>
<tr>
<td><code>INTEL_LRT_MODE</code></td>
<td>How to support Long-range thread mode in Verlet integration</td>
<td>
<dl>
<dt><code>threads</code> (default, if pthreads available)</dt>
<dt><code>none</code> (default, if pthreads not available)</dt>
<dt><code>c++11</code></dt>
</dl>
</td>
</tr>
</tbody>
</table>
@ -1503,6 +1516,16 @@ target API.
</dl>
</td>
</tr>
<tr>
<td><code>CUDA_MPS_SUPPORT</code> (CUDA only)</td>
<td>Enable tweaks for running with Nvidia CUDA Multi-process services daemon</td>
<td>
<dl>
<dt><code>on</code></dt>
<dt><code>off</code> (default)</dt>
</dl>
</td>
</tr>
<tr>
<td><code>BIN2C</code> (CUDA only)</td>
<td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

4
cmake/etc/profile.d/lammps.csh.in
View File

@ -1,2 +1,4 @@
# set environment for LAMMPS executables to find potential files
# set environment for LAMMPS and msi2lmp executables
# to find potential and force field files
if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@

7
cmake/etc/profile.d/lammps.sh.in
View File

@ -1,2 +1,5 @@
# set environment for LAMMPS executables to find potential files
export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
# set environment for LAMMPS and msi2lmp executables
# to find potential and force field files
LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

30
cmake/presets/all_off.cmake
View File

@ -1,21 +1,17 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns on all existing packages off. can be used to reset
# an existing package selection without losing any other settings
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

32
cmake/presets/all_on.cmake
View File

@ -1,21 +1,19 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns on all existing packages. using the combination
# this preset followed by the nolib.cmake preset should configure a
# LAMMPS binary, with as many packages included, that can be compiled
# with just a working C++ compiler and an MPI library.
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

17
cmake/presets/clang.cmake Normal file
View File

@ -0,0 +1,17 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)

71
cmake/presets/manual_selection.cmake
View File

@ -1,71 +0,0 @@
set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
set(PKG_BODY OFF CACHE BOOL "" FORCE)
set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
set(PKG_GPU OFF CACHE BOOL "" FORCE)
set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
set(PKG_KIM OFF CACHE BOOL "" FORCE)
set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
set(PKG_LATTE OFF CACHE BOOL "" FORCE)
set(PKG_LIB OFF CACHE BOOL "" FORCE)
set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
set(PKG_MC OFF CACHE BOOL "" FORCE)
set(PKG_MEAM OFF CACHE BOOL "" FORCE)
set(PKG_MISC OFF CACHE BOOL "" FORCE)
set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
set(PKG_MSCG OFF CACHE BOOL "" FORCE)
set(PKG_OPT OFF CACHE BOOL "" FORCE)
set(PKG_PERI OFF CACHE BOOL "" FORCE)
set(PKG_POEMS OFF CACHE BOOL "" FORCE)
set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
set(PKG_QEQ OFF CACHE BOOL "" FORCE)
set(PKG_REAX OFF CACHE BOOL "" FORCE)
set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
set(PKG_RIGID OFF CACHE BOOL "" FORCE)
set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
set(PKG_SNAP OFF CACHE BOOL "" FORCE)
set(PKG_SRD OFF CACHE BOOL "" FORCE)
set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
set(PKG_USER OFF CACHE BOOL "" FORCE)
set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

17
cmake/presets/mingw-cross.cmake Normal file
View File

@ -0,0 +1,17 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)

8
cmake/presets/minimal.cmake Normal file
View File

@ -0,0 +1,8 @@
# preset that turns on just a few, frequently used packages
# this will be compiled quickly and handle a lot of common inputs.
set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

15
cmake/presets/most.cmake Normal file
View File

@ -0,0 +1,15 @@
# preset that turns on a wide range of packages, some of which require
# external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

23
cmake/presets/nolib.cmake
View File

@ -1,21 +1,10 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent.
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

22
cmake/presets/std.cmake
View File

@ -1,22 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

26
cmake/presets/std_nolib.cmake
View File

@ -1,26 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
endforeach()

22
cmake/presets/user.cmake
View File

@ -1,22 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${USER_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

16
doc/Makefile
View File

@ -116,6 +116,13 @@ mobi: epub
@echo "Conversion finished. The MOBI manual file is created."
pdf: $(OBJECTS) $(ANCHORCHECK)
@(\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ../../; \
)
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
@ -136,13 +143,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
make && \
mv LAMMPS.pdf ../Manual.pdf && \
cd ../;
@(\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ../../; \
)
@rm -rf latex/_sources
@rm -rf latex/PDF
@rm -rf latex/USER
@ -211,7 +211,7 @@ $(VENV):
@( \
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install Sphinx; \
pip install Sphinx==1.7.6; \
deactivate;\
)

245
doc/lammps.1
View File

@ -1,40 +1,259 @@
.TH LAMMPS "2018-08-22"
.TH LAMMPS "11 April 2019" "2019-04-11"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
.SH SYNOPSIS
.B lmp
-in in.file
\-in <input file> [OPTIONS] ...
or
mpirun \-np 2
.B lmp
-in in.file
<input file> [OPTIONS] ...
or
.B lmp
\-r2data file.restart file.data
.SH DESCRIPTION
.B LAMMPS
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
materials (biomolecules, polymers) and solid-state materials (metals,
is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
.B LAMMPS
has potentials for soft
materials (bio-molecules, polymers) and solid-state materials (metals,
semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale.
See http://lammps.sandia.gov/ for documentation.
See https://lammps.sandia.gov/ for more information and documentation.
.SH EXECUTABLE NAME
The
.B LAMMPS
executable can have different names depending on how it was configured,
compiled and installed. It will be either
.B lmp
or
.B lmp_<machine name>.
The <machine name> suffix corresponds to the (machine specific) makefile
used to compile
.B LAMMPS
when using the conventional build process. When building
.B LAMMPS
using
.B CMake
this <machine name> parameter can be chosen arbitrarily at configuration
time, but more common is to just use
.B lmp
without a suffix. In this manpage we will use
.B lmp
to represent any of those names.
.SH OPTIONS
See https://lammps.sandia.gov/doc/Run_options.html for details on
command-line options.
.TP
\fB\-h\fR or \fB\-help\fR
Print a brief help summary and a list of settings and options compiled
into this executable. It also explicitly lists all LAMMPS styles
(atom_style, fix, compute, pair_style, bond_style, etc) available in
the specific executable. This can tell you if the command you want to
use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is used.
.TP
\fB\-e\fR or \fB\-echo\fR
Set the style of command echoing. The style can be
.B none
or
.B screen
or
.B log
or
.B both.
Depending on the style, each command read from the input script will
be echoed to the screen and/or logfile. This can be useful to figure
out which line of your script is causing an input error.
The default value is
.B log.
.TP
\fB\-i <input file>\fR or \fB\-in <input file>\fR
Specify a file to use as an input script. If it is not specified,
LAMMPS reads its script from standard input. This is a required
switch when running LAMMPS in multi-partition mode.
.TP
\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
Enable or disable general KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, this switch must
be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
details on this switch and its optional keyword value pairs are discussed
at: https://lammps.sandia.gov/doc/Run_options.html
.TP
\fB\-l <log file>\fR or \fB\-log <log file>\fR
Specify a log file for LAMMPS to write status information to.
The default value is "log.lammps". If the file name "none" is used,
\fBLAMMPS\fR will not write a log file. In multi-partition mode only
some high-level all-partition information is written to the "<log file>"
file, the remainder is written in a per-partition file "<log file>.N"
with "N" being the respective partition number, unless overridden
by the \-plog flag (see below).
.TP
\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
If used, this must be the first command-line argument after the
.B LAMMPS
executable name. It is only used when
.B LAMMPS
is launched by an mpirun command which also launches one or more
other executable(s) at the same time.
.B LAMMPS
and the other executable(s) perform an MPI_Comm_split(), each with
their own different colors, to split the MPI_COMM_WORLD communicator
for each executable to the subset of processors they are supposed to
be actually running on. Currently, this is only used in
.B LAMMPS
to perform client/server messaging with another application.
.B LAMMPS
can act as either a client or server (or both).
.TP
\fB\-nc\fR or \fB\-nocite\fR
Disable writing the "log.cite" file which is normally written to
list references for specific cite-able features used during a
.B LAMMPS
run.
.TP
\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
Invoke the \fBpackage\R command with <style> and optional arguments.
The syntax is the same as if the command appeared in an input script.
For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the
.B LAMMPS
manual for the "package" command. This switch can be used multiple
times, e.g. to set options for the USER-INTEL and USER-OMP packages
when used together. Along with the "-sf" or "-suffix" switch, this
is a convenient mechanism for invoking accelerator packages and their
options without having to edit an input script.
.TP
\fB\-p\fR or \fB\-partition\fR
Invoke
.B LAMMPS
in multi-partition mode. Without this,
.B LAMMPS
uses all P processors allocated via MPI to run a single simulation.
If this switch is used, the P processors are split into separate
partitions and each partition runs its own simulation. The arguments
to the switch specify the number of processors in each partition.
Arguments of the form "MxN" mean M partitions, each with N processors.
Arguments of the form "N" mean a single partition with N processors.
The sum of processors in all partitions must be equal P. Thus the
command “-partition 8x2 4 5” has 10 partitions and runs on a total
of 25 processors. Running with multiple partitions is required for
multi-replica simulations, where each replica runs on on one or more
few processors.
.TP
\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
Specify the base name for the per-partition log files in multi-partition
runs, where partition N writes log information to <basename>.N.
If basename is set to "none", then no per-partition log files are created.
This overrides the name specified in the \-log command-line option.
.TP
\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
Specify the base name for the per-partition screen files in multi-partition
runs, where partition N writes screen output to <basename>.N.
If basename is set to "none", then no per-partition screen files are created.
The default value is "screen" or whatever is set by the \-screen flag.
.TP
\fB\-r2data <restart file> [remap] <data file>\fR or
\fB\-restart2data <restart file> [remap] <data file>\fR
Convert <restart file> previously written by
.B LAMMPS
into a data file and immediately exit. This option has replaced the
external restart2data executable. Following <restart file>
argument, the optional word "remap" may be used. This has the
same effect like adding it to a "read_restart" command.
The syntax following the <data file> name is identical to the
arguments of the "write_data" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2dump <restart file> [remap] <dump file>\fR or
\fB\-restart2dump <restart file> [remap] <dump file>\fR
Convert <restart file> previously written by
.B LAMMPS
into a dump file and immediately exit. Following <restart file>
argument, the optional word "remap" may be used. This has the
same effect like adding it to a "read_restart" command.
The syntax following the <dump file> name is identical to the
arguments of the "dump" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B LAMMPS
to write its screen information to. By default, this will be
the standard output. If <file name> is "none", (most) screen
output will be suppressed. In multi-partition mode only
some high-level all-partition information is written to the
screen or "<file name>" file, the remainder is written in a
per-partition file "screen.N" or "<file name>.N"
with "N" being the respective partition number, and unless
overridden by the \-pscreen flag (see above).
.TP
\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
Use variants of various styles in the input, if they exist. This is
achieved by transparently trying to convert a style named <my/style>
into <my/style/suffix> if that latter style exists, but otherwise
fall back to the former. The most useful suffixes are "gpu",
"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
optional packages that LAMMPS can be built with. The hybrid suffix is
special, as it enables, having two suffixes tried (e.g. first "intel"
and then "omp") and thus requires two arguments. Along with the
"-package" command-line switch, this is a convenient mechanism for
invoking styles from accelerator packages and setting their options
without having to edit an input script.
See https://lammps.sandia.gov/doc/Run_options.html for additional
details and discussions on command-line options.
.SH LAMMPS BASICS
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set or change an
internal, read and parse a file, or run a simulation. Most commands
have default settings, which means you only need to use the command
if you wish to change the default.
The ordering of commands in an input script is usually not very important
unless a command like "run" is encountered, which starts some calculation
using the current internal state. Also, if a "pair_style" or "bond_style"
other similar style command is issued that has a different name from what
was previously active, it will replace the previous style and wipe out
all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group of a given name. Sometimes command B will use values
that can be set by command A. This means command A must precede command
B in the input to have the desired effect. Some commands must be issued
.B before
the simulation box is defined and others can only be issued
.B after.
Many input script errors are detected by
.B LAMMPS
and an ERROR or WARNING message is printed. The documentation for
each command lists restrictions on how the command can be used, and
the chapter on errors in the
.B LAMMPS
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2018 Sandia Corporation
© 2003--2019 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
it under the terms of the GNU General Public License version 2 as
published by the Free Software Foundation.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of

111
doc/msi2lmp.1 Normal file
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@ -0,0 +1,111 @@
.TH MSI2LMP "v3.9.9" "2018-11-05"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
.SH SYNOPSIS
.B msi2lmp
<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
.SH DESCRIPTION
.PP
.B MSI2LMP
is a tool bundled with LAMMPS to aide in the conversion of simulation
inputs from Biovia's Materials Studio software for use with LAMMPS.
It is a standalone program that generates a LAMMPS data file based on
the information in an MS .car file (atom coordinates), an .mdf file
(molecular topology and atom types) and an .frc (forcefield parameters)
file. The .car and .mdf files are specific to a molecular system while
the .frc file is specific to a forcefield (variant). The only coherency
needed between .frc and .car/.mdf files are the atom types.
.PP
.SH OPTIONS
.TP
\fB\<ROOTNAME>\fR
This has to be the first argument and is a
.B mandatory
argument. It defines the root of the file names; i.e. for a
.B <ROOTNAME>
of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
in the current working directory.
.B msi2lmp
will then read and process those files according to its remaining settings.
All other settins are optional and have defaults as listed.
.TP
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
The \-c or \-class option selects the force field class, i.e which pair
styles and bond styles and so on are required in the LAMMPS input file.
Class I or class 1 uses similar combination of functional forms as Amber
and Charmm force field and support the force fields
.B cvff
and
.B clayff.
Class II or class 2 corresponds to the more complex force fields
.B COMPASS
and
.B pcff.
Class O or class 0 finally is an experimental and incomplete extension
and supports generating output for
.B OPLS-AA
.TP
\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
The \-c or \-frc option allows the selection of the force field parameter
file
.B<ffname>.frc.
Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
i.e. it starts with a '.' or a '/', then this absolute path is used to read
the force field, otherwise
.B msi2lmp
will look in the folder pointed to by the environment variable
$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
directory. The extension '.frc' is appended, if missing.
Default is to look for the cvff.frc force field file.
.TP
\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
Selects the amount of information messages about the progress of the
conversion printed to the screen.
.B <loglevel>
can be a number from 0 (silent except for errors) to 3 (very detailed).
.TP
\fB\-i\fR, \fB\-ignore\fR,
Ignore errors about missing parameters and use 0.0 for the respective
force constants making these no-ops. Is correct to be used for a few
molecules and settings, but often an indication, that either the atom
type assignment have errors, or the force field file is missing entries.
.TP
\fB\-n\fR, \fB\-nocenter\fR,
Do not center the box around the (geometrical) center of the atoms,
but around the origin. Default is to recenter.
.TP
\fB\-o\fR, \fB\-oldstyle\fR,
Write out a data file without style hint comments to be compatible
with old LAMMPS versions. Default is to write out those comments.
.TP
\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
Shift the entire system (box and coordinates) by a vector
(default: 0.0 0.0 0.0).
.TP
.SH EXAMPLES
msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
msi2lmp benzene-class1 -c I
msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as
published by the Free Software Foundation.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

8
doc/src/Build_cmake.txt
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@ -28,7 +28,7 @@ Makefile(s). Example:
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
cmake ../cmake \[options ...\] # configuration with (command-line) cmake
cmake \[options ...\] ../cmake # configuration with (command-line) cmake
make # compilation :pre
The cmake command will detect available features, enable selected
@ -41,7 +41,8 @@ If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
ccache (= Compiler Cache) software may speed up repeated compilation
even more.
After compilation, you can optionally copy the LAMMPS executable and
library into your system folders (by default under $HOME/.local) with:
@ -108,7 +109,8 @@ command-line options. Several useful ones are:
-D CMAKE_BUILD_TYPE=type # type = Release or Debug
-G output # style of output CMake generates
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir :pre
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring :pre
All the LAMMPS-specific -D variables that a LAMMPS build supports are
described on the pages linked to from the "Build"_Build.html doc page.

83
doc/src/Build_extras.txt
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@ -82,17 +82,19 @@ which GPU hardware to build for.
[CMake build]:
-D GPU_API=value # value = opencl (default) or cuda
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is Cuda-compiler dependent, but typically sm_20
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# yes (default) or no :pre
-D GPU_API=value # value = opencl (default) or cuda
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is Cuda-compiler dependent, but typically sm_20
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default) :pre
GPU_ARCH settings for different GPU hardware is as follows:
@ -169,16 +171,18 @@ used to build the GPU library.
KIM package :h4,link(kim)
To build with this package, the KIM library must be downloaded and
built on your system. It must include the KIM models that you want to
use with LAMMPS.
To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS. If you want to use the "kim_query"_kim_query.html
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
Note that in LAMMPS lingo, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file. Also note that installing the KIM API
library with all its models, may take around 30 min to build. Of
course you only need to do that once.
specific EAM potential file. Also note that downloading and installing
the KIM API library with all its models, may take a long time (10s of
minutes to hours) to build. Of course you only need to do that once.
See the list of KIM model drivers here:
https://openkim.org/browse/model-drivers/alphabetical
@ -193,7 +197,7 @@ https://openkim.org/browse/models/by-model-drivers
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
environment variable so that libkim-api-v2 can be found.
environment variable so that libkim-api can be found.
[Traditional make]:
@ -855,23 +859,34 @@ file.
USER-INTEL package :h4,link(user-intel)
To build with this package, you must choose which hardware you want to
build for, either Intel CPUs or Intel KNLs. You should also typically
"install the USER-OMP package"_#user-omp, as it can be used in tandem
with the USER-INTEL package to good effect, as explained on the "Speed
intel"_Speed_intel.html doc page.
build for, either x86 CPUs or Intel KNLs in offload mode. You should
also typically "install the USER-OMP package"_#user-omp, as it can be
used in tandem with the USER-INTEL package to good effect, as explained
on the "Speed intel"_Speed_intel.html doc page.
[CMake build]:
-D INTEL_ARCH=value # value = cpu (default) or knl
-D BUILD_OMP=yes # also required to build with the USER-INTEl package :pre
-D INTEL_LRT_MODE=value # value = threads, none, or c++11 :pre
Requires an Intel compiler as well as the Intel TBB and MKL libraries.
In Long-range thread mode (LRT) a modified verlet style is used, that
operates the Kspace calculation in a separate thread concurrently to
other calculations. This has to be enabled in the "package intel"_package.html
command at runtime. With the setting "threads" it used the pthreads
library, while c++11 will use the built-in thread support of C++11
compilers. The option "none" skips compilation of this feature. The
default is to use "threads" if pthreads is available and otherwise "none".
Best performance is achieved with Intel hardware, Intel compilers, as well as
the Intel TBB and MKL libraries. However, the code also compiles, links, and
runs with other compilers and without TBB and MKL.
[Traditional make]:
Choose which hardware to compile for in Makefile.machine via the
following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu* and
Makefile.knl files for examples.
Makefile.knl files for examples. and src/USER-INTEL/README for
additional information.
For CPUs:
@ -893,7 +908,17 @@ USER-MOLFILE package :h4,link(user-molfile)
[CMake build]:
No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes :pre
Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
the molfile plugin header files. These should match the ABI of the
plugin files used, and thus one typically sets them to include
folder of the local VMD installation in use. LAMMPS ships with a
couple of default header files that correspond to a popular VMD
version, usually the latest release.
[Traditional make]:
@ -902,7 +927,11 @@ loading library libdl.a that is typically present on all systems. It
is required for LAMMPS to link with this package. If the setting is
not valid for your system, you will need to edit the Makefile.lammps
file. See lib/molfile/README and lib/molfile/Makefile.lammps for
details.
details. It is also possible to configure a different folder with
the VMD molfile plugin header files. LAMMPS ships with a couple of
default headers, but these are not compatible with all VMD versions,
so it is often best to change this setting to the location of the
same include files of the local VMD installation in use.
:line

39
doc/src/Build_package.txt
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@ -149,26 +149,41 @@ system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs.
cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake |
enable all packages |
cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
disable all packages |
cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
enable just a few core packages |
cmake -C ../cmake/presets/most.cmake \[OPTIONS\] ../cmake |
enable most common packages |
cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake |
disable packages that do require extra libraries or tools |
cmake -C ../cmake/presets/clang.cmake \[OPTIONS\] ../cmake |
change settings to use the Clang compilers by default |
cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake |
enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l)
NOTE: Running cmake this way manipulates the variable cache in your
current build directory. You can combine presets and options with
multiple cmake runs.
current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running
cmake with new flags.
[Example:]
# build LAMMPS with all "standard" packages which don't
# use libraries and enable GPU package
# build LAMMPS with most commonly used packages, but then remove
# those requiring additional library or tools, but still enable
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on . :pre
# to reset the package selection from above to the default of no packages
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake . :pre
:line
[Make shortcuts for installing many packages]:

13
doc/src/Build_settings.txt
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@ -57,10 +57,10 @@ FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
# default is FFT_PACK_ARRAY if not specified
FFT_INC = -I/usr/local/include
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre
@ -179,8 +179,11 @@ e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the "compute
msd"_compute_msd.html command, to be faulty.
Note that the USER-ATC package is not currently compatible with the
"bigbig" setting.
Note that the USER-ATC package and the USER-INTEL package are currently
not compatible with the "bigbig" setting. Also, there are limitations
when using the library interface. Some functions with known issues
have been replaced by dummy calls printing a corresponding error rather
than crashing randomly or corrupting data.
Also note that the GPU package requires its lib/gpu library to be
compiled with the same size setting, or the link will fail. A CMake

15
doc/src/Build_windows.txt
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@ -51,11 +51,10 @@ provides a unix/linux interface to low-level Windows functions, so LAMMPS
can be compiled on Windows. The necessary (minor) modifications to LAMMPS
are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. The CMake build system is untested
for this; you will have to request that makefiles are generated and
manually set the compiler.
the old build system is provided. Using CMake for this mode of compilation
is untested and not likely to work.
When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
@ -79,7 +78,13 @@ probably the currently best tested and supported way to build LAMMPS
executables for Windows. There are makefiles provided for the
traditional build system, but CMake has also been successfully tested
using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines.
with the cross-compiler environment on Fedora machines. A CMake preset
selecting all packages compatible with this cross-compilation build
is provided. You likely need to disable the GPU package unless you
download and install the contents of the pre-compiled "OpenCL ICD loader
library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz
into your MinGW64 cross-compiler environment. The cross-compilation
currently will only produce non-MPI serial binaries.
Please keep in mind, though, that this only applies to compiling LAMMPS.
Whether the resulting binaries do work correctly is no tested by the

2
doc/src/Commands_all.txt
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@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kim_query"_kim_query.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
@ -78,6 +79,7 @@ An alphabetic list of all general LAMMPS commands.
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"min_style spin"_min_spin.html,
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,

3
doc/src/Commands_fix.txt
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@ -61,6 +61,7 @@ OPT.
"edpd/source"_fix_dpd_source.html,
"efield"_fix_efield.html,
"ehex"_fix_ehex.html,
"electron/stopping"_fix_electron_stopping.html,
"enforce2d (k)"_fix_enforce2d.html,
"eos/cv"_fix_eos_cv.html,
"eos/table"_fix_eos_table.html,
@ -224,7 +225,7 @@ OPT.
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
"wall/gran (o)"_fix_wall_gran.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,

1
doc/src/Commands_pair.txt
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@ -98,6 +98,7 @@ OPT.
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (o)"_pair_gran.html,
"gran/hooke/history (ko)"_pair_gran.html,
"granular"_pair_granular.html,
"gw"_pair_gw.html,
"gw/zbl"_pair_gw.html,
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,

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@ -0,0 +1,13 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
\nonumber
\end{equation}
\end{varwidth}
\end{document}

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@ -0,0 +1,14 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
{\Delta t}_{\rm max} = \frac{2\pi}{\kappa
\left|\vec{\omega}_{\rm max} \right|}
\nonumber
\end{equation}
\end{varwidth}
\end{document}

2
doc/src/Howto.txt
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@ -148,7 +148,7 @@ END_RST -->
<!-- HTML_ONLY -->
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)

87
doc/src/Howto_bioFF.txt
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@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
CHARMM, AMBER, and DREIDING force fields :h3
CHARMM, AMBER, COMPASS, and DREIDING force fields :h3
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an input data file
via the "read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
"bond_coeff"_bond_coeff.html and so on. See the "Tools"_Tools.html doc
page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input.
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
field.
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER
force field. See "(Sun)"_#howto-Sun for a description of the COMPASS
force field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
command's documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"angle_style"_angle_charmm.html charmm
@ -44,28 +46,54 @@ documentation for the formula it computes.
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
released in March 2017. We recommend they be used instead of the
older {charmm} styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
doc pages.
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
in March 2017. We recommend they be used instead of the older {charmm}
styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
pages.
COMPASS is a general force field for atomistic simulation of common
organic molecules, inorganic small molecules, and polymers which was
developed using ab initio and empirical parameterization techniques.
See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA’s Materials Studio
files. Please note that the msi2lmp tool is very old and largely
unmaintained, so it does not support all features of Materials Studio
provided force field files, especially additions during the last decade.
You should watch the output carefully and compare results, where
possible. See "(Sun)"_#howto-Sun for a description of the COMPASS force
field.
These interaction styles listed below compute force field formulas that
are consistent with the COMPASS force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_class2.html class2
"angle_style"_angle_class2.html class2
"dihedral_style"_dihedral_class2.html class2
"improper_style"_improper_class2.html class2 :ul
"pair_style"_pair_class2.html lj/class2
"pair_style"_pair_class2.html lj/class2/coul/cut
"pair_style"_pair_class2.html lj/class2/coul/long :ul
"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul
DREIDING is a generic force field developed by the "Goddard
group"_http://www.wag.caltech.edu at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).
predicting structures and dynamics of organic, biological and main-group
inorganic molecules. The philosophy in DREIDING is to use general force
constants and geometry parameters based on simple hybridization
considerations, rather than individual force constants and geometric
parameters that depend on the particular combinations of atoms involved
in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
bond term"_pair_hbond_dreiding.html to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F).
See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
The interaction styles listed below compute force field formulas that
are consistent with the DREIDING force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
@ -100,6 +128,9 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(howto-Sun)
[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998).
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

11
doc/src/Howto_library.txt
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@ -166,9 +166,6 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
void lammps_scatter_atoms(void *, char *, int, int, void *)
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int) :pre
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each calling processor. The scatter
@ -176,6 +173,11 @@ functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to individual atoms, which may be
owned by different processors.
IMPORTANT NOTE: These functions are not compatible with the
-DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions
that result in an error message and abort will be substituted
instead of resulting in random crashes and memory corruption.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
@ -196,6 +198,9 @@ those values to each atom in the system. The
lammps_scatter_atoms_subset() function takes a subset of IDs as an
argument and only scatters those values to the owning atoms.
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int) :pre
The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and
velocities and image flags. It uses the coords of each atom to assign

31
doc/src/Howto_pylammps.txt
View File

@ -57,6 +57,17 @@ library is then loaded by the Python interface. In this example we enable the
MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
output support enabled.
Step 1a: For the CMake based build system, the steps are:
mkdir $LAMMPS_DIR/build-shared
cd $LAMMPS_DIR/build-shared :pre
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
make :pre
Step 1b: For the legacy, make based build system, the steps are:
cd $LAMMPS_DIR/src :pre
# add packages if necessary
@ -68,10 +79,9 @@ make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS
Step 2: Installing the LAMMPS Python package :h6
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation.
that package into your current Python installation with:
cd $LAMMPS_DIR/python
python install.py :pre
make install-python :pre
NOTE: Recompiling the shared library requires re-installing the Python package
@ -94,14 +104,21 @@ apt-get install python-virtualenv :pre
Creating a virtualenv with lammps installed :h6
# create virtualenv name 'testing' :pre
# create virtualenv named 'testing'
virtualenv $HOME/python/testing :pre
# activate 'testing' environment
source testing/bin/activate :pre
source $HOME/python/testing/bin/activate :pre
Now configure and compile the LAMMPS shared library as outlined above.
When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
# install LAMMPS package in virtualenv
(testing) cd $LAMMPS_DIR/python
(testing) python install.py :pre
(testing) make install-python :pre
# install other useful packages
(testing) pip install matplotlib jupyter mpi4py :pre

6
doc/src/Howto_tip3p.txt
View File

@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
TIP3P water model :h3
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -60,6 +60,10 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(howto-tip3p)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Jorgensen1)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="28 Feb 2019 version">
<META NAME="docnumber" CONTENT="29 Mar 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
28 Feb 2019 version :c,h2
29 Mar 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

2
doc/src/Packages_details.txt
View File

@ -341,6 +341,8 @@ KIM package :link(PKG-KIM),h4
A "pair_style kim"_pair_kim.html command which is a wrapper on the
Knowledge Base for Interatomic Models (KIM) repository of interatomic
potentials, enabling any of them to be used in LAMMPS simulations.
Also a "kim_query"_kim_query.html command, which allows to query
the OpenKIM database for stored properties.
To use this package you must have the KIM library available on your
system.

69
doc/src/Python_install.txt
View File

@ -12,16 +12,23 @@ Installing LAMMPS in Python :h3
For Python to invoke LAMMPS, there are 2 files it needs to know about:
python/lammps.py
src/liblammps.so :ul
liblammps.so or liblammps.dylib :ul
Lammps.py is the Python wrapper on the LAMMPS library interface.
Liblammps.so is the shared LAMMPS library that Python loads, as
described above.
The python source code in lammps.py is the Python wrapper on the
LAMMPS library interface. The liblammps.so or liblammps.dylib file
is the shared LAMMPS library that Python loads dynamically.
You can insure Python can find these files in one of two ways:
You can achieve that Python can find these files in one of two ways:
set two environment variables
run the python/install.py script :ul
set two environment variables pointing to the location in the source tree
run "make install-python" or run the python/install.py script explicitly :ul
When calling "make install-python" LAMMPS will try to install the
python module and the shared library into the python site-packages folders;
either the system-wide ones, or the local users ones (in case of insufficient
permissions for the global install). Python will then find the module
and shared library file automatically. The exact location of these folders
depends on your python version and your operating system.
If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like
@ -30,42 +37,28 @@ this to your ~/.cshrc file, one line for each of the two files:
setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the
python/lammps.py file.
On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.
For Bourne/Korn shells accordingly into the corresponding files using
the "export" shell builtin.
You can invoke install.py from the python directory as
If you use "make install-python" or the python/install.py script, you need
to invoke it every time you rebuild LAMMPS (as a shared library) or
make changes to the python/lammps.py file, so that the site-packages
files are updated with the new version.
% python install.py \[libdir\] \[pydir\] :pre
If the default settings of "make install-python" are not what you want,
you can invoke install.py from the python directory manually as
The optional libdir is where to copy the LAMMPS shared library to; the
default is /usr/local/lib. The optional pydir is where to copy the
lammps.py file to; the default is the site-packages directory of the
version of Python that is running the install script.
% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre
Note that libdir must be a location that is in your default
LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a
location that Python looks in by default for imported modules, like
its site-packages dir. If you want to copy these files to
non-standard locations, such as within your own user space, you will
need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
accordingly, as above.
The -m flag points to the lammps.py python module file to be installed,
the -l flag points to the LAMMPS shared library file to be installed,
the -v flag points to the version.h file in the LAMMPS source
and the optional -d flag to a custom (legacy) installation folder :ul
If the install.py script does not allow you to copy files into system
directories, prefix the python command with "sudo". If you do this,
make sure that the Python that root runs is the same as the Python you
run. E.g. you may need to do something like
% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
You can also invoke install.py from the make command in the src
directory as
% make install-python :pre
In this mode you cannot append optional arguments. Again, you may
need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
If you use a legacy installation folder, you will need to set your
PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment
variables accordingly, as described above.
Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see "this section"_Python_shlib.html), you will

19
doc/src/Python_overview.txt
View File

@ -13,11 +13,11 @@ Overview of Python and LAMMPS :h3
LAMMPS can work together with Python in three ways. First, Python can
wrap LAMMPS through the its "library interface"_Howto_library.html, so
that a Python script can create one or more instances of LAMMPS and
launch one or more simulations. In Python lingo, this is "extending"
Python with LAMMPS.
launch one or more simulations. In Python lingo, this is called
"extending" Python with a LAMMPS module.
Second, a lower-level Python interface can be used indirectly through
provided PyLammps and IPyLammps wrapper classes, written in Python.
the provided PyLammps and IPyLammps wrapper classes, written in Python.
These wrappers try to simplify the usage of LAMMPS in Python by
providing an object-based interface to common LAMMPS functionality.
They also reduces the amount of code necessary to parameterize LAMMPS
@ -25,11 +25,12 @@ scripts through Python and make variables and computes directly
accessible.
Third, LAMMPS can use the Python interpreter, so that a LAMMPS
input script can invoke Python code directly, and pass information
back-and-forth between the input script and Python functions you
write. This Python code can also callback to LAMMPS to query or change
its attributes. In Python lingo, this is "embedding" Python in
LAMMPS. When used in this mode, Python can perform operations that
the simple LAMMPS input script syntax cannot.
input script or styles can invoke Python code directly, and pass
information back-and-forth between the input script and Python
functions you write. This Python code can also callback to LAMMPS
to query or change its attributes through the LAMMPS Python module
mentioned above. In Python lingo, this is "embedding" Python in
LAMMPS. When used in this mode, Python can perform script operations
that the simple LAMMPS input script syntax can not.

4
doc/src/Run_options.txt
View File

@ -79,7 +79,7 @@ stdin.
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, as described
in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable
running with the KOKKOS-enabled styles the package provides. If the
running with KOKKOS-enabled styles the package provides. If the
switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or USER-OMP packages, for testing or benchmarking purposes.
@ -448,7 +448,7 @@ partition screen files file.N.
[-suffix style args] :link(suffix)
Use variants of various styles if they exist. The specified style can
be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
be {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
refer to optional packages that LAMMPS can be built with, as described
in "Accelerate performance"_Speed.html. The "gpu" style corresponds to the
GPU package, the "intel" style to the USER-INTEL package, the "kk"

6
doc/src/Speed_intel.txt
View File

@ -24,7 +24,7 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
Angle Styles: charmm, harmonic :ulb,l
Bond Styles: fene, fourier, harmonic :l
Dihedral Styles: charmm, harmonic, opls :l
Dihedral Styles: charmm, fourier, harmonic, opls :l
Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
Improper Styles: cvff, harmonic :l
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
@ -34,6 +34,10 @@ rebo, sw, tersoff :l
K-Space Styles: pppm, pppm/disp :l
:ule
IMPORTANT NOTE: None of the styles in the USER-INTEL package currently
support computing per-atom stress. If any compute or fix in your
input requires it, LAMMPS will abort with an error message.
[Speed-ups to expect:]
The speedups will depend on your simulation, the hardware, which

2
doc/src/commands_list.txt
View File

@ -53,6 +53,7 @@ Commands :h1
include
info
jump
kim_query
kspace_modify
kspace_style
label
@ -61,6 +62,7 @@ Commands :h1
mass
message
min_modify
min_spin
min_style
minimize
molecule

7
doc/src/compute.txt
View File

@ -54,9 +54,10 @@ local quantities have the word "local" in their style,
e.g. {bond/local}. Styles with neither "atom" or "local" in their
style produce global quantities.
Note that a single compute produces either global or per-atom or local
quantities, but never more than one of these (with only a few
exceptions, as documented by individual compute commands).
Note that a single compute can produce either global or per-atom or
local quantities, but not both global and per-atom. It can produce
local quantities in tandem with global or per-atom quantities. The
compute doc page will explain.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The

7
doc/src/fix.txt
View File

@ -83,8 +83,10 @@ not in the specified fix group. Local quantities are calculated by
each processor based on the atoms it owns, but there may be zero or
more per atoms.
Note that a single fix may produces either global or per-atom or local
quantities (or none at all), but never more than one of these.
Note that a single fix can produce either global or per-atom or local
quantities (or none at all), but not both global and per-atom. It can
produce local quantities in tandem with global or per-atom quantities.
The fix doc page will explain.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
@ -199,6 +201,7 @@ accelerated styles exist.
"edpd/source"_fix_dpd_source.html -
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -

19
doc/src/fix_ave_histo.txt
View File

@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
{mode} arg = {scalar} or {vector}
scalar = all input values are scalars
vector = all input values are vectors
{kind} arg = {global} or {peratom} or {local}
{file} arg = filename
filename = name of file to output histogram(s) to
{ave} args = {one} or {running} or {window}
@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities. Inputs of
different kinds (e.g. global and per-atom) cannot be mixed. Atom
attributes are per-atom vector values. See the doc page for
individual "compute" and "fix" commands to see what kinds of
quantities they generate.
quantities they generate. See the optional {kind} keyword below for
how to force the fix ave/histo command to disambiguate if necessary.
Note that the output of this command is a single histogram for all
input values combined together, not one histogram per input value.
@ -231,6 +233,14 @@ keyword is set to {vector}, then all input values must be global or
per-atom or local vectors, or columns of global or per-atom or local
arrays.
The {kind} keyword only needs to be set if a compute or fix produces
more than one kind of output (global, per-atom, local). If this is
not the case, then LAMMPS will determine what kind of input is
provided and whether all the input arguments are consistent. If a
compute or fix produces more than one kind of output, the {kind}
keyword should be used to specify which output will be used. The
remaining input arguments must still be consistent.
The {beyond} keyword determines how input values that fall outside the
{lo} to {hi} bounds are treated. Values such that {lo} <= value <=
{hi} are assigned to one bin. Values on a bin boundary are assigned
@ -240,7 +250,7 @@ If {beyond} is set to {end} then values < {lo} are counted in the
first bin and values > {hi} are counted in the last bin. If {beyond}
is set to {extend} then two extra bins are created, so that there are
Nbins+2 total bins. Values < {lo} are counted in the first bin and
values > {hi} are counted in the last bin (Nbins+1). Values between
values > {hi} are counted in the last bin (Nbins+2). Values between
{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1. The
"coordinate" stored and printed for these two extra bins is {lo} and
{hi}.
@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
[Default:] none
The option defaults are mode = scalar, ave = one, start = 0, no file
output, beyond = ignore, and title 1,2,3 = strings as described above.
The option defaults are mode = scalar, kind = figured out from input
arguments, ave = one, start = 0, no file output, beyond = ignore, and
title 1,2,3 = strings as described above.

4
doc/src/fix_bond_react.txt
View File

@ -385,6 +385,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
When fix bond/react is 'unfixed,' all internally-created groups are
deleted. Therefore, fix bond/react can only be unfixed after unfixing
all other fixes that use any group created by fix bond/react.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if

165
doc/src/fix_electron_stopping.txt Normal file
View File

@ -0,0 +1,165 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix electron/stopping command :h3
[Syntax:]
fix ID group-ID electron/stopping Ecut file keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
electron/stopping = style name of this fix command :l
Ecut = minimum kinetic energy for electronic stopping (energy units) :l
file = name of the file containing the electronic stopping power table :l
zero or more keyword/value pairs may be appended to args :l
keyword = {region} or {minneigh} :l
{region} value = region-ID
region-ID = region, whose atoms will be affected by this fix
{minneigh} value = minneigh
minneigh = minimum number of neighbors an atom to have stopping applied :pre
:ule
[Examples:]
fix el all electron/stopping 10.0 elstop-table.txt
fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk :pre
[Description:]
This fix implements inelastic energy loss for fast projectiles in solids. It
applies a friction force to fast moving atoms to slow them down due to
"electronic stopping"_#elstopping (energy lost via electronic collisions per
unit of distance). This fix should be used for simulation of irradiation
damage or ion implantation, where the ions can lose noticeable amounts of
energy from electron excitations. If the electronic stopping power is not
considered, the simulated range of the ions can be severely overestimated
("Nordlund98"_#Nordlund98, "Nordlund95"_#Nordlund95).
The electronic stopping is implemented by applying a friction force
to each atom as:
\begin\{equation\}
\vec\{F\}_i = \vec\{F\}^0_i - \frac\{\vec\{v\}_i\}\{\|\vec\{v\}_i\|\} \cdot S_e
\end\{equation\}
where \(\vec\{F\}_i\) is the resulting total force on the atom.
\(\vec\{F\}^0_i\) is the original force applied to the atom, \(\vec\{v\}_i\) is
its velocity and \(S_e\) is the stopping power of the ion.
NOTE: In addition to electronic stopping, atomic cascades and irradiation
simulations require the use of an adaptive timestep (see
"fix dt/reset"_fix_dt_reset.html) and the repulsive ZBL potential (see
"ZBL"_pair_zbl.html potential) or similar. Without these settings the
interaction between the ion and the target atoms will be faulty. It is also
common to use in such simulations a thermostat ("fix_nvt"_fix_nh.html) in
the borders of the simulation cell.
NOTE: This fix removes energy from fast projectiles without depositing it as a
heat to the simulation cell. Such implementation might lead to the unphysical
results when the amount of energy deposited to the electronic system is large,
e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or
higher) or multiple projectiles. You could compensate energy loss by coupling
bulk atoms with some thermostat or control heat transfer between electronic and
atomic subsystems with the two-temperature model ("fix_ttm"_fix_ttm.html).
At low velocities the electronic stopping is negligible. The electronic
friction is not applied to atoms whose kinetic energy is smaller than {Ecut},
or smaller than the lowest energy value given in the table in {file}.
Electronic stopping should be applied only when a projectile reaches bulk
material. This fix scans neighbor list and excludes atoms with fewer than
{minneigh} neighbors (by default one). If the pair potential cutoff is large,
minneigh should be increased, though not above the number of nearest neighbors
in bulk material. An alternative is to disable the check for neighbors by
setting {minneigh} to zero and using the {region} keyword. This is necessary
when running simulations of cluster bombardment.
If the {region} keyword is used, the atom must also be in the specified
geometric "region"_region.html in order to have electronic stopping applied to
it. This is useful if the position of the bulk material is fixed. By default
the electronic stopping is applied everywhere in the simulation cell.
:line
The energy ranges and stopping powers are read from the file {file}.
Lines starting with {#} and empty lines are ignored. Otherwise each
line must contain exactly [N+1] numbers, where [N] is the number of atom
types in the simulation.
The first column is the energy for which the stopping powers on that
line apply. The energies must be sorted from the smallest to the largest.
The other columns are the stopping powers \(S_e\) for each atom type,
in ascending order, in force "units"_units.html. The stopping powers for
intermediate energy values are calculated with linear interpolation between
2 nearest points.
For example:
# This is a comment
# atom-1 atom-2
# eV eV/Ang eV/Ang # units metal
10 0 0
250 60 80
750 100 150 :pre
If an atom which would have electronic stopping applied to it has a
kinetic energy higher than the largest energy given in {file}, LAMMPS
will exit with an error message.
The stopping power depends on the energy of the ion and the target
material. The electronic stopping table can be obtained from
scientific publications, experimental databases or by using
"SRIM"_#SRIM software. Other programs such as "CasP"_#CasP or
"PASS"_#PASS can calculate the energy deposited as a function
of the impact parameter of the ion; these results can be used
to derive the stopping power.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html options are not supported.
This fix computes a global scalar, which can be accessed by various
"output commands"_Howto_output.html. The scalar is the total energy
loss from electronic stopping applied by this fix since the start of
the latest run. It is considered "intensive".
The {start/stop} keywords of the "run"_run.html command have no effect
on this fix.
[Restrictions:]
This pair style is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build package"_Build_package.html
doc page for more info.
[Default:]
The default is no limitation by region, and minneigh = 1.
:line
:link(elstopping)
[(electronic stopping)] Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
:link(Nordlund98)
[(Nordlund98)] Nordlund, Kai, et al. Physical Review B 57.13 (1998): 7556.
:link(Nordlund95)
[(Nordlund95)] Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
:link(SRIM)
[(SRIM)] SRIM webpage: http://www.srim.org/
:link(CasP)
[(CasP)] CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
:link(PASS)
[(PASS)] PASS webpage: https://www.sdu.dk/en/DPASS

45
doc/src/fix_hyper_global.txt
View File

@ -102,7 +102,7 @@ Bi = exp(beta * Vij(max)) :pre
where beta = 1/kTequil, and {Tequil} is the temperature of the system
and an argument to this fix. Note that Bi >= 1 at every step.
NOTE: To run GHD, the input script must also use the "fix
NOTE: To run a GHD simulation, the input script must also use the "fix
langevin"_fix_langevin.html command to thermostat the atoms at the
same {Tequil} as specified by this fix, so that the system is running
constant-temperature (NVT) dynamics. LAMMPS does not check that this
@ -166,9 +166,9 @@ correctly. There will just be fewer events because the hyper time
NOTE: If you have no physical intuition as to the smallest barrier
height in your system, a reasonable strategy to determine the largest
{Vmax} you can use for an LHD model, is to run a sequence of
{Vmax} you can use for a GHD model, is to run a sequence of
simulations with smaller and smaller {Vmax} values, until the event
rate does not change.
rate does not change (as a function of hyper time).
The {Tequil} argument is the temperature at which the system is
simulated; see the comment above about the "fix
@ -177,7 +177,8 @@ beta term in the exponential factor that determines how much boost is
achieved as a function of the bias potential.
In general, the lower the value of {Tequil} and the higher the value
of {Vmax}, the more boost will be achievable by the GHD algorithm.
of {Vmax}, the more time boost will be achievable by the GHD
algorithm.
:line
@ -190,41 +191,43 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of the bias potential to the the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and global vector of length 11, which
This fix computes a global scalar and global vector of length 12, which
can be accessed by various "output commands"_Howto_output.html. The
scalar is the magnitude of the bias potential (energy units) applied on
the current timestep. The vector stores the following quantities:
1 = boost factor on this step (unitless)
2 = max strain Eij of any bond on this step (unitless)
2 = max strain Eij of any bond on this step (absolute value, unitless)
3 = ID of first atom in the max-strain bond
4 = ID of second atom in the max-strain bond
5 = average # of bonds/atom on this step :ul
6 = fraction of timesteps with bias = 0.0 during this run
7 = max drift distance of any atom during this run (distance units)
8 = max bond length during this run (distance units) :ul
6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
7 = fraction of timesteps where the biased bond has negative strain during this run
8 = max drift distance of any atom during this run (distance units)
9 = max bond length during this run (distance units) :ul
9 = cumulative hyper time since fix was defined (time units)
10 = cumulative count of event timesteps since fix was defined
11 = cumulative count of atoms in events since fix was defined :ul
10 = cumulative hyper time since fix was defined (time units)
11 = cumulative count of event timesteps since fix was defined
12 = cumulative count of atoms in events since fix was defined :ul
The first 5 quantities are for the current timestep. Quantities 6-8
are for the current hyper run. Quantities 9-11 are cumulative across
multiple runs (since the fix was defined in the input script).
The first 5 quantities are for the current timestep. Quantities 6-9
are for the current hyper run. They are reset each time a new hyper
run is performed. Quantities 19-12 are cumulative across multiple
runs (since the point in the input script the fix was defined).
For value 7, drift is the distance an atom moves between timesteps
when the bond list is reset, i.e. between events. Atoms involved in
an event will typically move the greatest distance since others are
typically oscillating around their lattice site.
For value 8, drift is the distance an atom moves between two quenched
states when the second quench determines an event has occurred. Atoms
involved in an event will typically move the greatest distance since
others typically remain near their original quenched position.
For value 10, events are checked for by the "hyper"_hyper.html command
For value 11, events are checked for by the "hyper"_hyper.html command
once every {Nevent} timesteps. This value is the count of those
timesteps on which one (or more) events was detected. It is NOT the
number of distinct events, since more than one event may occur in the
same {Nevent} time window.
For value 11, each time the "hyper"_hyper.html command checks for an
For value 12, each time the "hyper"_hyper.html command checks for an
event, it invokes a compute to flag zero or more atoms as
participating in one or more events. E.g. atoms that have displaced
more than some distance from the previous quench state. Value 11 is

225
doc/src/fix_hyper_local.txt
View File

@ -22,10 +22,9 @@ Dcut = minimum distance between boosted bonds (distance units) :l
alpha = boostostat relaxation time (time units) :l
Btarget = desired time boost factor (unitless) :l
zero or more keyword/value pairs may be appended :l
keyword = {lost} or {check/bias} or {check/coeff}
{lostbond} value = error/warn/ignore
{check/bias} values = Nevery error/warn/ignore
{check/coeff} values = Nevery error/warn/ignore :pre
keyword = {check/ghost} or {check/bias} :l
{check/ghost} values = none
{check/bias} values = Nevery error/warn/ignore :pre
:ule
[Examples:]
@ -65,8 +64,8 @@ To understand this description, you should first read the description
of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
doc page. This description of LHD builds on the GHD description.
The definition of bonds, Eij, and Emax are the same for GHD and LHD.
The formulas for Vij(max) and Fij(max) are also the same except for a
The definition of bonds and Eij are the same for GHD and LHD. The
formulas for Vij(max) and Fij(max) are also the same except for a
pre-factor Cij, explained below.
The bias energy Vij applied to a bond IJ with maximum strain is
@ -117,11 +116,11 @@ where Vkl(max) is the bias energy of the maxstrain bond KL within bond
IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
of the system and an argument to this fix.
NOTE: To run LHD, the input script must also use the "fix
langevin"_fix_langevin.html command to thermostat the atoms at the
same {Tequil} as specified by this fix, so that the system is running
constant-temperature (NVT) dynamics. LAMMPS does not check that this
is done.
NOTE: To run an LHD simulation, the input script must also use the
"fix langevin"_fix_langevin.html command to thermostat the atoms at
the same {Tequil} as specified by this fix, so that the system is
running constant-temperature (NVT) dynamics. LAMMPS does not check
that this is done.
Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
otherwise it is not. But regardless, the boost factor Bij can be
@ -216,20 +215,20 @@ each pair. E.g. something like 2x the cutoff of the interatomic
potential. In practice a {Dcut} value of ~10 Angstroms seems to work
well for many solid-state systems.
NOTE: You must also insure that ghost atom communication is performed
for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
distance one or more atoms move (between quenched states) to be
considered an "event". It is an argument to the "compute
event/displace" command used to detect events. By default the ghost
communication distance is set by the pair_style cutoff, which will
typically be < {Dcut}. The "comm_modify cutoff"_comm_modify.html
command can be used to set the ghost cutoff explicitly, e.g.
NOTE: You should insure that ghost atom communication is performed for
a distance of at least {Dcut} + {cutevent} = the distance one or more
atoms move (between quenched states) to be considered an "event". It
is an argument to the "compute event/displace" command used to detect
events. By default the ghost communication distance is set by the
pair_style cutoff, which will typically be < {Dcut}. The "comm_modify
cutoff"_comm_modify.html command should be used to override the ghost
cutoff explicitly, e.g.
comm_modify cutoff 12.0 :pre
This fix does not know the {cutevent} parameter, but uses half the
bond length as an estimate to warn if the ghost cutoff is not long
enough.
Note that this fix does not know the {cutevent} parameter, but uses
half the {cutbond} parameter as an estimate to warn if the ghost
cutoff is not long enough.
As described above the {alpha} argument is a pre-factor in the
boostostat update equation for each bond's Cij prefactor. {Alpha} is
@ -269,7 +268,30 @@ NOTE: If you have no physical intuition as to the smallest barrier
height in your system, a reasonable strategy to determine the largest
{Btarget} you can use for an LHD model, is to run a sequence of
simulations with smaller and smaller {Btarget} values, until the event
rate does not change.
rate does not change (as a function of hyper time).
:line
Here is additional information on the optional keywords for this fix.
The {check/ghost} keyword turns on extra computation each timestep to
compute statistics about ghost atoms used to determine which bonds to
bias. The output of these stats are the vector values 14 and 15,
described below. If this keyword is not enabled, the output
of the stats will be zero.
The {check/bias} keyword turns on extra computation and communication
to check if any biased bonds are closer than {Dcut} to each other,
which should not be the case if LHD is operating correctly. Thus it
is a debugging check. The {Nevery} setting determines how often the
check is made. The {error}, {warn}, or {ignore} setting determines
what is done if the count of too-close bonds is not zero. Either the
code will exit, or issue a warning, or silently tally the count. The
count can be output as vector value 17, as described below. If this
keyword is not enabled, the output of that statistic will be 0.
Note that both of these computations are costly, hence they are only
enabled by these keywords.
:line
@ -282,95 +304,120 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of the bias potential to the the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and global vector of length 23,
which can be accessed by various "output
commands"_Howto_output.html. The scalar is the magnitude of
the bias potential (energy units) applied on the current timestep,
summed over all biased bonds. The vector stores the following
quantities:
This fix computes a global scalar and global vector of length 21,
which can be accessed by various "output commands"_Howto_output.html.
The scalar is the magnitude of the bias potential (energy units)
applied on the current timestep, summed over all biased bonds. The
vector stores the following quantities:
1 = # of biased bonds on this step
2 = max strain Eij of any bond on this step (unitless)
3 = average bias potential for all biased bonds on this step (energy units)
2 = max strain Eij of any bond on this step (absolute value, unitless)
3 = average bias coeff for all bonds on this step (unitless)
4 = average # of bonds/atom on this step
5 = average neighbor bonds/bond on this step within {Dcut} :ul
6 = fraction of steps and bonds with no bias during this run
7 = max drift distance of any atom during this run (distance units)
8 = max bond length during this run (distance units)
9 = average # of biased bonds/step during this run
10 = average bias potential for all biased bonds during this run (energy units)
11 = max bias potential for any biased bond during this run (energy units)
12 = min bias potential for any biased bond during this run (energy units)
13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
15 = count of ghost neighbor atoms not found on reneighbor steps during this run
16 = count of lost bond partners during this run
17 = average bias coeff for lost bond partners during this run
18 = count of bias overlaps found during this run
19 = count of non-matching bias coefficients found during this run :ul
6 = max bond length during this run (distance units)
7 = average # of biased bonds/step during this run
8 = fraction of biased bonds with no bias during this run
9 = fraction of biased bonds with negative strain during this run
10 = average bias coeff for all bonds during this run (unitless)
11 = min bias coeff for any bond during this run (unitless)
12 = max bias coeff for any bond during this run (unitless)
20 = cumulative hyper time since fix created (time units)
21 = cumulative count of event timesteps since fix created
22 = cumulative count of atoms in events since fix created
23 = cumulative # of new bonds since fix created :ul
13 = max drift distance of any bond atom during this run (distance units)
14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
16 = count of ghost atoms that could not be found on reneighbor steps during this run
17 = count of bias overlaps (< Dcut) found during this run
18 = cumulative hyper time since fix created (time units)
19 = cumulative count of event timesteps since fix created
20 = cumulative count of atoms in events since fix created
21 = cumulative # of new bonds formed since fix created :ul
The first quantities (1-5) are for the current timestep. Quantities
6-19 are for the current hyper run. They are reset each time a new
hyper run is performed. Quantities 20-23 are cumulative across
multiple runs (since the fix was defined in the input script).
6-17 are for the current hyper run. They are reset each time a new
hyper run is performed. Quantities 18-21 are cumulative across
multiple runs (since the point in the input script the fix was
defined).
For value 6, the numerator is a count of all biased bonds on every
For value 8, the numerator is a count of all biased bonds on each
timestep whose bias energy = 0.0 due to Eij >= {qfactor}. The
denominator is the count of all biased bonds on all timesteps.
For value 7, drift is the distance an atom moves between timesteps
when the bond list is reset, i.e. between events. Atoms involved in
an event will typically move the greatest distance since others are
typically oscillating around their lattice site.
For value 9, the numerator is a count of all biased bonds on each
timestep with negative strain. The denominator is the count of all
biased bonds on all timesteps.
For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
of any bond it is part of, and it is checked for ghost atoms within
the bond neighbor cutoff.
Values 13-17 are mostly useful for debugging and diagnostic purposes.
Values 15-19 are mostly useful for debugging and diagnostic purposes.
For value 13, drift is the distance an atom moves between two quenched
states when the second quench determines an event has occurred. Atoms
involved in an event will typically move the greatest distance since
others typically remain near their original quenched position.
For values 15-17, it is possible that a ghost atom owned by another
processor will move far enough (e.g. as part of an event-in-progress)
that it will no longer be within the communication cutoff distance for
acquiring ghost atoms. Likewise it may be a ghost atom bond partner
that cannot be found because it has moved too far. These values count
those occurrences. Because they typically involve atoms that are part
of events, they do not usually indicate bad dynamics. Value 16 is the
average bias coefficient for bonds where a partner atom was lost.
For values 14-16, neighbor atoms in the full neighbor list with cutoff
{Dcut} may be ghost atoms outside a processor's sub-box. Before the
next event occurs they may move further than {Dcut} away from the
sub-box boundary. Value 14 is the furthest (from the sub-box) any
ghost atom in the neighbor list with maxstrain < {qfactor} was
accessed during the run. Value 15 is the same except that the ghost
atom's maxstrain may be >= {qfactor}, which may mean it is about to
participate in an event. Value 16 is a count of how many ghost atoms
could not be found on reneighbor steps, presumably because they moved
too far away due to their participation in an event (which will likely
be detected at the next quench).
For value 18, no two bonds should be biased if they are within a
Typical values for 14 and 15 should be slightly larger than {Dcut},
which accounts for ghost atoms initially at a {Dcut} distance moving
thermally before the next event takes place.
Note that for values 14 and 15 to be computed, the optional keyword
{check/ghost} must be specified. Otherwise these values will be zero.
This is because computing them incurs overhead, so the values are only
computed if requested.
Value 16 should be zero or small. As explained above a small count
likely means some ghost atoms were participating in their own events
and moved a longer distance. If the value is large, it likely means
the communication cutoff for ghosts is too close to {Dcut} leading to
many not-found ghost atoms before the next event. This may lead to a
reduced number of bonds being selected for biasing, since the code
assumes those atoms are part of highly strained bonds. As explained
above, the "comm_modify cutoff"_comm_modify.html command can be used
to set a longer cutoff.
For value 17, no two bonds should be biased if they are within a
{Dcut} distance of each other. This value should be zero, indicating
that no pair of bonds "overlap", meaning they are closer than {Dcut}
from each other.
that no pair of biased bonds are closer than {Dcut} from each other.
For value 19, the same bias coefficient is stored by both atoms in an
IJ bond. This value should be zero, indicating that for all bonds,
each atom in the bond stores the a bias coefficient with the same
value.
Note that for values 17 to be computed, the optional keyword
{check/bias} must be specified and it determines how often this check
is performed. This is because performing the check incurs overhead,
so if only computed as often as requested.
Value 20 is simply the specified {boost} factor times the number of
timestep times the timestep size.
The result at the end of the run is the cumulative total from every
timestep the check was made. Note that the value is a count of atoms
in bonds which found other atoms in bonds too close, so it is almost
always an over-count of the number of too-close bonds.
For value 21, events are checked for by the "hyper"_hyper.html command
Value 18 is simply the specified {boost} factor times the number of
timesteps times the timestep size.
For value 19, events are checked for by the "hyper"_hyper.html command
once every {Nevent} timesteps. This value is the count of those
timesteps on which one (or more) events was detected. It is NOT the
number of distinct events, since more than one event may occur in the
same {Nevent} time window.
For value 22, each time the "hyper"_hyper.html command checks for an
For value 20, each time the "hyper"_hyper.html command checks for an
event, it invokes a compute to flag zero or more atoms as
participating in one or more events. E.g. atoms that have displaced
more than some distance from the previous quench state. Value 22 is
more than some distance from the previous quench state. Value 20 is
the cumulative count of the number of atoms participating in any of
the events that were found.
Value 23 tallies the number of new bonds created by the bond reset
Value 21 tallies the number of new bonds created by the bond reset
operation. Bonds between a specific I,J pair of atoms may persist for
the entire hyperdynamics simulation if neither I or J are involved in
an event.
@ -378,6 +425,16 @@ an event.
The scalar and vector values calculated by this fix are all
"intensive".
This fix also computes a local vector of length the number of bonds
currently in the system. The value for each bond is its Cij prefactor
(bias coefficient). These values can be can be accessed by various
"output commands"_Howto_output.html. A particularly useful one is the
"fix ave/histo"_fix_ave_histo.html command which can be used to
histogram the Cij values to see if they are distributed reasonably
close to 1.0, which indicates a good choice of {Vmax}.
The local values calculated by this fix are unitless.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
@ -392,7 +449,9 @@ doc page for more info.
"hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
[Default:] None
[Default:]
The check/ghost and check/bias keywords are not enabled by default.
:line

101
doc/src/fix_wall_gran.txt
View File

@ -7,22 +7,24 @@
:line
fix wall/gran command :h3
fix wall/gran/omp command :h3
[Syntax:]
fix ID group-ID wall/gran fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... :pre
fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/gran = style name of this fix command :l
fstyle = style of force interactions between particles and wall :l
possible choices: hooke, hooke/history, hertz/history :pre
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
dampflag = 0 or 1 if tangential damping force is excluded or included :l
possible choices: hooke, hooke/history, hertz/history, granular :pre
fstyle_params = parameters associated with force interaction style :l
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
args = list of arguments for a particular style :l
{xplane} or {yplane} or {zplane} args = lo hi
@ -44,7 +46,10 @@ keyword = {wiggle} or {shear} :l
fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 :pre
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
[Description:]
@ -54,31 +59,40 @@ close enough to touch it.
The nature of the wall/particle interactions are determined by the
{fstyle} setting. It can be any of the styles defined by the
"pair_style granular"_pair_gran.html commands. Currently this is
{hooke}, {hooke/history}, or {hertz/history}. The equation for the
force between the wall and particles touching it is the same as the
corresponding equation on the "pair_style granular"_pair_gran.html doc
page, in the limit of one of the two particles going to infinite
radius and mass (flat wall). Specifically, delta = radius - r =
overlap of particle with wall, m_eff = mass of particle, and the
effective radius of contact = RiRj/Ri+Rj is just the radius of the
particle.
"pair_style gran/*"_pair_gran.html or the more general "pair_style
granular"_pair_granular.html" commands. Currently the options are
{hooke}, {hooke/history}, or {hertz/history} for the former, and
{granular} with all the possible options of the associated
{pair_coeff} command for the latter. The equation for the force
between the wall and particles touching it is the same as the
corresponding equation on the "pair_style gran/*"_pair_gran.html and
"pair_style_granular"_pair_granular.html doc pages, in the limit of
one of the two particles going to infinite radius and mass (flat
wall). Specifically, delta = radius - r = overlap of particle with
wall, m_eff = mass of particle, and the effective radius of contact =
RiRj/Ri+Rj is set to the radius of the particle.
The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
have the same meaning and units as those specified with the
"pair_style granular"_pair_gran.html commands. This means a NULL can
be used for either {Kt} or {gamma_t} as described on that page. If a
"pair_style gran/*"_pair_gran.html commands. This means a NULL can be
used for either {Kt} or {gamma_t} as described on that page. If a
NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
{Kn}. If a NULL is used for {gamma_t}, then a default value is used
where {gamma_t} = 1/2 {gamma_n}.
All the model choices for cohesion, tangential friction, rolling
friction and twisting friction supported by the "pair_style
granular"_pair_granular.html through its {pair_coeff} command are also
supported for walls. These are discussed in greater detail on the doc
page for "pair_style granular"_pair_granular.html.
Note that you can choose a different force styles and/or different
values for the 6 wall/particle coefficients than for particle/particle
values for the wall/particle coefficients than for particle/particle
interactions. E.g. if you wish to model the wall as a different
material.
NOTE: As discussed on the doc page for "pair_style
granular"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
gran/*"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
different equation for Hertzian interactions. This means Hertizian
wall/particle interactions have also changed. They now include a
sqrt(radius) term which was not present before. Also the previous
@ -108,14 +122,14 @@ Optionally, the wall can be moving, if the {wiggle} or {shear}
keywords are appended. Both keywords cannot be used together.
For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the
"fix move"_fix_move.html command. This is useful in packing
simulations of granular particles. The arguments to the {wiggle}
keyword specify a dimension for the motion, as well as it's
{amplitude} and {period}. Note that if the dimension is in the plane
of the wall, this is effectively a shearing motion. If the dimension
is perpendicular to the wall, it is more of a shaking motion. A
{zcylinder} wall can only be wiggled in the z dimension.
the oscillations of particles which can be specified by the "fix
move"_fix_move.html command. This is useful in packing simulations of
granular particles. The arguments to the {wiggle} keyword specify a
dimension for the motion, as well as it's {amplitude} and {period}.
Note that if the dimension is in the plane of the wall, this is
effectively a shearing motion. If the dimension is perpendicular to
the wall, it is more of a shaking motion. A {zcylinder} wall can only
be wiggled in the z dimension.
Each timestep, the position of a wiggled wall in the appropriate {dim}
is set according to this equation:
@ -137,28 +151,6 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the
@ -188,6 +180,7 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
"fix move"_fix_move.html,
"fix wall/gran/region"_fix_wall_gran_region.html,
"pair_style granular"_pair_gran.html
"pair_style gran/*"_pair_gran.html
"pair_style granular"_pair_granular.html
[Default:] none

76
doc/src/fix_wall_gran_region.txt
View File

@ -10,24 +10,30 @@ fix wall/gran/region command :h3
[Syntax:]
fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/region = style name of this fix command :l
fstyle = style of force interactions between particles and wall :l
possible choices: hooke, hooke/history, hertz/history :pre
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
dampflag = 0 or 1 if tangential damping force is excluded or included :l
possible choices: hooke, hooke/history, hertz/history, granular :pre
fstyle_params = parameters associated with force interaction style :l
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
region-ID = region whose boundary will act as wall :l,ule
[Examples:]
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
[Description:]
@ -42,8 +48,8 @@ Here are snapshots of example models using this command.
Corresponding input scripts can be found in examples/granregion.
Click on the images to see a bigger picture. Movies of these
simulations are "here on the Movies
page"_http://lammps.sandia.gov/movies.html#granregion of the
LAMMPS web site.
page"_http://lammps.sandia.gov/movies.html#granregion of the LAMMPS
web site.
:image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
:image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
@ -123,12 +129,16 @@ to make the two faces differ by epsilon in their position.
The nature of the wall/particle interactions are determined by the
{fstyle} setting. It can be any of the styles defined by the
"pair_style granular"_pair_gran.html commands. Currently this is
{hooke}, {hooke/history}, or {hertz/history}. The equation for the
force between the wall and particles touching it is the same as the
corresponding equation on the "pair_style granular"_pair_gran.html doc
page, but the effective radius is calculated using the radius of the
particle and the radius of curvature of the wall at the contact point.
"pair_style gran/*"_pair_gran.html or the more general "pair_style
granular"_pair_granular.html" commands. Currently the options are
{hooke}, {hooke/history}, or {hertz/history} for the former, and
{granular} with all the possible options of the associated
{pair_coeff} command for the latter. The equation for the force
between the wall and particles touching it is the same as the
corresponding equation on the "pair_style gran/*"_pair_gran.html and
"pair_style_granular"_pair_granular.html doc pages, but the effective
radius is calculated using the radius of the particle and the radius
of curvature of the wall at the contact point.
Specifically, delta = radius - r = overlap of particle with wall,
m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
@ -141,12 +151,18 @@ particle.
The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
have the same meaning and units as those specified with the
"pair_style granular"_pair_gran.html commands. This means a NULL can
be used for either {Kt} or {gamma_t} as described on that page. If a
"pair_style gran/*"_pair_gran.html commands. This means a NULL can be
used for either {Kt} or {gamma_t} as described on that page. If a
NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
{Kn}. If a NULL is used for {gamma_t}, then a default value is used
where {gamma_t} = 1/2 {gamma_n}.
All the model choices for cohesion, tangential friction, rolling
friction and twisting friction supported by the "pair_style
granular"_pair_granular.html through its {pair_coeff} command are also
supported for walls. These are discussed in greater detail on the doc
page for "pair_style granular"_pair_granular.html.
Note that you can choose a different force styles and/or different
values for the 6 wall/particle coefficients than for particle/particle
interactions. E.g. if you wish to model the wall as a different
@ -154,9 +170,9 @@ material.
[Restart, fix_modify, output, run start/stop, minimize info:]
Similar to "fix wall/gran"_fix_wall_gran.html command, this fix
writes the shear friction state of atoms interacting with the wall to
"binary restart files"_restart.html, so that a simulation can continue
Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes
the shear friction state of atoms interacting with the wall to "binary
restart files"_restart.html, so that a simulation can continue
correctly if granular potentials with shear "history" effects are
being used. This fix also includes info about a moving region in the
restart file. See the "read_restart"_read_restart.html command for
@ -170,14 +186,14 @@ So you must re-define your region and if it is a moving region, define
its motion attributes in a way that is consistent with the simulation
that wrote the restart file. In particular, if you want to change the
region motion attributes (e.g. its velocity), then you should ensure
the position/orientation of the region at the initial restart
timestep is the same as it was on the timestep the restart file was
written. If this is not possible, you may need to ignore info in the
restart file by defining a new fix wall/gran/region command in your
restart script, e.g. with a different fix ID. Or if you want to keep
the shear history info but discard the region motion information, you
can use the same fix ID for fix wall/gran/region, but assign it a
region with a different region ID.
the position/orientation of the region at the initial restart timestep
is the same as it was on the timestep the restart file was written.
If this is not possible, you may need to ignore info in the restart
file by defining a new fix wall/gran/region command in your restart
script, e.g. with a different fix ID. Or if you want to keep the
shear history info but discard the region motion information, you can
use the same fix ID for fix wall/gran/region, but assign it a region
with a different region ID.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for

1
doc/src/fixes.txt
View File

@ -40,6 +40,7 @@ Fixes :h1
fix_dt_reset
fix_efield
fix_ehex
fix_electron_stopping
fix_enforce2d
fix_eos_cv
fix_eos_table

46
doc/src/kim_query.txt Normal file
View File

@ -0,0 +1,46 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
kim_query command :h3
[Syntax:]
kim_query variable query_function web_query_flags :pre
variable = name of a (string style) variable where the result of the query is stored
query_function = name of the OpenKIM web API query function to be used
web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
[Examples:]
kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
[Description:]
The kim_query command allows to retrieve properties from the OpenKIM
through a web query. The result is stored in a string style
"variable"_variable.html, the name of which must be given as the first
argument of the kim_query command. The second required argument is the
name of the actual query function (e.g. {get_test_result}). All following
arguments are parameters handed over to the web query in the format
{keyword=value}. The list of supported keywords and the type of how
the value has to be encoded depends on the query function used. This
mirrors the functionality available on the OpenKIM webpage at
"https://query.openkim.org"_https://query.openkim.org/
[Restrictions:]
This command is part of the KIM package. It is only enabled if
LAMMPS was built with that package. Furthermore, its correct
functioning depends on compiling LAMMPS with libcurl support.
See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
"pair_style kim"_pair_kim.html, "variable"_variable.html

4
doc/src/lammps.book
View File

@ -167,6 +167,7 @@ if.html
include.html
info.html
jump.html
kim_query.html
label.html
lattice.html
log.html
@ -174,6 +175,7 @@ mass.html
message.html
min_modify.html
min_style.html
min_spin.html
minimize.html
molecule.html
neb.html
@ -263,6 +265,7 @@ fix_drude_transform.html
fix_dt_reset.html
fix_efield.html
fix_ehex.html
fix_electron_stopping.html
fix_enforce2d.html
fix_eos_cv.html
fix_eos_table.html
@ -578,6 +581,7 @@ pair_extep.html
pair_gauss.html
pair_gayberne.html
pair_gran.html
pair_granular.html
pair_gromacs.html
pair_gw.html
pair_ilp_graphene_hbn.html

19
doc/src/min_modify.txt
View File

@ -13,11 +13,15 @@ min_modify command :h3
min_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {dmax} or {line}
keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
{dmax} value = max
max = maximum distance for line search to move (distance units)
{line} value = {backtrack} or {quadratic} or {forcezero}
backtrack,quadratic,forcezero = style of linesearch to use :pre
backtrack,quadratic,forcezero = style of linesearch to use
{alpha_damp} value = damping
damping = fictitious Gilbert damping for spin minimization (adim)
{discrete_factor} value = factor
factor = discretization factor for adaptive spin timestep (adim) :pre
:ule
[Examples:]
@ -65,6 +69,17 @@ difference of two large values (energy before and energy after) and
that difference may be smaller than machine epsilon even if atoms
could move in the gradient direction to reduce forces further.
Keywords {alpha_damp} and {discrete_factor} only make sense when
a "min_spin"_min_spin.html command is declared.
Keyword {alpha_damp} defines an analog of a magnetic Gilbert
damping. It defines a relaxation rate toward an equilibrium for
a given magnetic system.
Keyword {discrete_factor} defines a discretization factor for the
adaptive timestep used in the {spin} minimization.
See "min_spin"_min_spin.html for more information about those
quantities.
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
[Restrictions:] none
[Related commands:]

65
doc/src/min_spin.txt Normal file
View File

@ -0,0 +1,65 @@
"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
min_style spin command :h3
[Syntax:]
min_style spin :pre
[Examples:]
min_style spin :pre
[Description:]
Apply a minimization algorithm to use when a "minimize"_minimize.html
command is performed.
Style {spin} defines a damped spin dynamics with an adaptive
timestep, according to:
:c,image(Eqs/min_spin_damping.jpg)
with lambda a damping coefficient (similar to a Gilbert
damping).
Lambda can be defined by setting the {alpha_damp} keyword with the
"min_modify"_min_modify.html command.
The minimization procedure solves this equation using an
adaptive timestep. The value of this timestep is defined
by the largest precession frequency that has to be solved in the
system:
:c,image(Eqs/min_spin_timestep.jpg)
with {|omega|_{max}} the norm of the largest precession frequency
in the system (across all processes, and across all replicas if a
spin/neb calculation is performed).
Kappa defines a discretization factor {discrete_factor} for the
definition of this timestep.
{discrete_factor} can be defined with the "min_modify"_min_modify.html
command.
NOTE: The {spin} style replaces the force tolerance by a torque
tolerance. See "minimize"_minimize.html for more explanation.
[Restrictions:]
This minimization procedure is only applied to spin degrees of
freedom for a frozen lattice configuration.
[Related commands:]
"min_style"_min_style.html, "minimize"_minimize.html,
"min_modify"_min_modify.html
[Default:]
The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
10.0.

7
doc/src/min_style.txt
View File

@ -11,11 +11,12 @@ min_style command :h3
min_style style :pre
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
[Examples:]
min_style cg
min_style spin
min_style fire :pre
[Description:]
@ -61,6 +62,10 @@ the velocity non-parallel to the current force vector. The velocity
of each atom is initialized to 0.0 by this style, at the beginning of
a minimization.
Style {spin} is a damped spin dynamics with an adaptive
timestep.
See the "min/spin"_min_spin.html doc page for more information.
Either the {quickmin} and {fire} styles are useful in the context of
nudged elastic band (NEB) calculations via the "neb"_neb.html command.

7
doc/src/minimize.txt
View File

@ -103,6 +103,13 @@ the line search fails because the step distance backtracks to 0.0
the number of outer iterations or timesteps exceeds {maxiter}
the number of total force evaluations exceeds {maxeval} :ul
NOTE: the "minimization style"_min_style.html {spin} replaces
the force tolerance {ftol} by a torque tolerance.
The minimization procedure stops if the 2-norm (length) of the
global torque vector (defined as the cross product between the
spins and their precession vectors omega) is less than {ftol},
or if any of the other criteria are met.
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
a general criterion for exiting a minimization, that is a calculation
performed on the state of the current system, as defined by an

765
doc/src/pair_granular.txt Normal file
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@ -0,0 +1,765 @@
<script type="text/javascript"
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
</script>
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style granular command :h3
[Syntax:]
pair_style granular cutoff :pre
cutoff = global cutoff (optional). See discussion below. :ul
[Examples:]
pair_style granular
pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre
pair_style granular
pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
pair_style granular
pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
pair_style granular
pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
pair_style granular
pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall
pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre
[Description:]
The {granular} styles support a variety of options for the normal,
tangential, rolling and twisting forces resulting from contact between
two granular particles. This expands on the options offered by the
"pair gran/*"_pair_gran.html pair styles. The total computed forces
and torques are the sum of various models selected for the normal,
tangential, rolling and twisting modes of motion.
All model choices and parameters are entered in the
"pair_coeff"_pair_coeff.html command, as described below. Unlike
e.g. "pair gran/hooke"_pair_gran.html, coefficient values are not
global, but can be set to different values for different combinations
of particle types, as determined by the "pair_coeff"_pair_coeff.html
command. If the contact model choice is the same for two particle
types, the mixing for the cross-coefficients can be carried out
automatically. This is shown in the second example, where model
choices are the same for type 1 - type 1 as for type 2 - type2
interactions, but coefficients are different. In this case, the
coefficients for type 2 - type interactions can be determined from
mixing rules discussed below. For additional flexibility,
coefficients as well as model forms can vary between particle types,
as shown in the third example: type 1- type 1 interactions are based
on a Hertzian normal contact model and 2-2 interactions are based on a
DMT cohesive model (see below). In that example, 1-1 and 2-2
interactions have different model forms, in which case mixing of
coefficients cannot be determined, so 1-2 interactions must be
explicitly defined via the {pair_coeff 1 2} command, otherwise an
error would result.
:line
The first required keyword for the {pair_coeff} command is the normal
contact model. Currently supported options for normal contact models
and their required arguments are:
{hooke} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
{hertz} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
{hertz/material} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\)
{dmt} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\)
{jkr} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\) :ol
Here, \(k_n\) is spring stiffness (with units that depend on model
choice, see below); \(\eta_\{n0\}\) is a damping prefactor (or, in its
place a coefficient of restitution \(e\), depending on the choice of
damping mode, see below); E is Young's modulus in units of
{force}/{length}^2, i.e. {pressure}; \(\nu\) is Poisson's ratio and
\(\gamma\) is a surface energy density, in units of
{energy}/{length}^2.
For the {hooke} model, the normal, elastic component of force acting
on particle {i} due to contact with particle {j} is given by:
\begin\{equation\}
\mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\}
\end\{equation\}
Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} =
\mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two
particle centers (note the i-j ordering so that \(F_\{ne\}\) is
positive for repulsion), and \(\mathbf\{n\} =
\frac\{\mathbf\{r\}_\{ij\}\}\{\|\mathbf\{r\}_\{ij\}\|\}\). Therefore,
for {hooke}, the units of the spring constant \(k_n\) are
{force}/{distance}, or equivalently {mass}/{time^2}.
For the {hertz} model, the normal component of force is given by:
\begin\{equation\}
\mathbf\{F\}_\{ne, Hertz\} = k_N R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
\end\{equation\}
Here, \(R_\{eff\} = \frac\{R_i R_j\}\{R_i + R_j\}\) is the effective
radius, denoted for simplicity as {R} from here on. For {hertz}, the
units of the spring constant \(k_n\) are {force}/{length}^2, or
equivalently {pressure}.
For the {hertz/material} model, the force is given by:
\begin\{equation\}
\mathbf\{F\}_\{ne, Hertz/material\} = \frac\{4\}\{3\} E_\{eff\} R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
\end\{equation\}
Here, \(E_\{eff\} = E = \left(\frac\{1-\nu_i^2\}\{E_i\} +
\frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}\) is the effective Young's
modulus, with \(\nu_i, \nu_j \) the Poisson ratios of the particles of
types {i} and {j}. Note that if the elastic modulus and the shear
modulus of the two particles are the same, the {hertz/material} model
is equivalent to the {hertz} model with \(k_N = 4/3 E_\{eff\}\)
The {dmt} model corresponds to the
"(Derjaguin-Muller-Toporov)"_#DMT1975 cohesive model, where the force
is simply Hertz with an additional attractive cohesion term:
\begin\{equation\}
\mathbf\{F\}_\{ne, dmt\} = \left(\frac\{4\}\{3\} E R^\{1/2\}\delta_\{ij\}^\{3/2\} - 4\pi\gamma R\right)\mathbf\{n\}
\end\{equation\}
The {jkr} model is the "(Johnson-Kendall-Roberts)"_#JKR1971 model,
where the force is computed as:
\begin\{equation\}
\label\{eq:force_jkr\}
\mathbf\{F\}_\{ne, jkr\} = \left(\frac\{4Ea^3\}\{3R\} - 2\pi a^2\sqrt\{\frac\{4\gamma E\}\{\pi a\}\}\right)\mathbf\{n\}
\end\{equation\}
Here, {a} is the radius of the contact zone, related to the overlap
\(\delta\) according to:
\begin\{equation\}
\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}
\end\{equation\}
LAMMPS internally inverts the equation above to solve for {a} in terms
of \(\delta\), then solves for the force in the previous
equation. Additionally, note that the JKR model allows for a tensile
force beyond contact (i.e. for \(\delta < 0\)), up to a maximum of
\(3\pi\gamma R\) (also known as the 'pull-off' force). Note that this
is a hysteretic effect, where particles that are not contacting
initially will not experience force until they come into contact
\(\delta \geq 0\); as they move apart and (\(\delta < 0\)), they
experience a tensile force up to \(3\pi\gamma R\), at which point they
lose contact.
:line
In addition, the normal force is augmented by a damping term of the
following general form:
\begin\{equation\}
\mathbf\{F\}_\{n,damp\} = -\eta_n \mathbf\{v\}_\{n,rel\}
\end\{equation\}
Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i)
\cdot \mathbf\{n\}\) is the component of relative velocity along
\(\mathbf\{n\}\).
The optional {damping} keyword to the {pair_coeff} command followed by
a keyword determines the model form of the damping factor \(\eta_n\),
and the interpretation of the \(\eta_\{n0\}\) or \(e\) coefficients
specified as part of the normal contact model settings. The {damping}
keyword and corresponding model form selection may be appended
anywhere in the {pair coeff} command. Note that the choice of damping
model affects both the normal and tangential damping (and depending on
other settings, potentially also the twisting damping). The options
for the damping model currently supported are:
{velocity}
{viscoelastic}
{tsuji} :ol
If the {damping} keyword is not specified, the {viscoelastic} model is
used by default.
For {damping velocity}, the normal damping is simply equal to the
user-specified damping coefficient in the {normal} model:
\begin\{equation\}
\eta_n = \eta_\{n0\}\
\end\{equation\}
Here, \(\gamma_n\) is the damping coefficient specified for the normal
contact model, in units of {mass}/{time},
The {damping viscoelastic} model is based on the viscoelastic
treatment of "(Brilliantov et al)"_#Brill1996, where the normal
damping is given by:
\begin\{equation\}
\eta_n = \eta_\{n0\}\ a m_\{eff\}
\end\{equation\}
Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a}
is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models
except {jkr}, for which it is given implicitly according to \(delta =
a^2/R - 2\sqrt\{\pi \gamma a/E\}\). In this case, \eta_\{n0\}\ is in
units of 1/({time}*{distance}).
The {tsuji} model is based on the work of "(Tsuji et
al)"_#Tsuji1992. Here, the damping coefficient specified as part of
the normal model is interpreted as a restitution coefficient
\(e\). The damping constant \(\eta_n\) is given by:
\begin\{equation\}
\eta_n = \alpha (m_\{eff\}k_n)^\{1/2\}
\end\{equation\}
For normal contact models based on material parameters, \(k_n =
4/3Ea\). The parameter \(\alpha\) is related to the restitution
coefficient {e} according to:
\begin\{equation\}
\alpha = 1.2728-4.2783e+11.087e^2-22.348e^3+27.467e^4-18.022e^5+4.8218e^6
\end\{equation\}
The dimensionless coefficient of restitution \(e\) specified as part
of the normal contact model parameters should be between 0 and 1, but
no error check is performed on this.
The total normal force is computed as the sum of the elastic and
damping components:
\begin\{equation\}
\mathbf\{F\}_n = \mathbf\{F\}_\{ne\} + \mathbf\{F\}_\{n,damp\}
\end\{equation\}
:line
The {pair_coeff} command also requires specification of the tangential
contact model. The required keyword {tangential} is expected, followed
by the model choice and associated parameters. Currently supported
tangential model choices and their expected parameters are as follows:
{linear_nohistory} : \(x_\{\gamma,t\}\), \(\mu_s\)
{linear_history} : \(k_t\), \(x_\{\gamma,t\}\), \(\mu_s\)
{mindlin} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\)
{mindlin_rescale} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\) :ol
Here, \(x_\{\gamma,t\}\) is a dimensionless multiplier for the normal
damping \(\eta_n\) that determines the magnitude of the tangential
damping, \(\mu_t\) is the tangential (or sliding) friction
coefficient, and \(k_t\) is the tangential stiffness coefficient.
For {tangential linear_nohistory}, a simple velocity-dependent Coulomb
friction criterion is used, which mimics the behavior of the {pair
gran/hooke} style. The tangential force (\mathbf\{F\}_t\) is given by:
\begin\{equation\}
\mathbf\{F\}_t = -min(\mu_t F_\{n0\}, \|\mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
\end\{equation\}
The tangential damping force \(\mathbf\{F\}_\mathrm\{t,damp\}\) is given by:
\begin\{equation\}
\mathbf\{F\}_\mathrm\{t,damp\} = -\eta_t \mathbf\{v\}_\{t,rel\}
\end\{equation\}
The tangential damping prefactor \(\eta_t\) is calculated by scaling
the normal damping \(\eta_n\) (see above):
\begin\{equation\}
\eta_t = -x_\{\gamma,t\} \eta_n
\end\{equation\}
The normal damping prefactor \(\eta_n\) is determined by the choice of
the {damping} keyword, as discussed above. Thus, the {damping}
keyword also affects the tangential damping. The parameter
\(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the
literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
"Tsuji et al"_#Tsuji1992, "Silbert et al"_#Silbert2001). The relative
tangential velocity at the point of contact is given by
\(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i +
R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} =
\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r =
\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force
is \(\mathbf\{t\} =
\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\).
The normal force value \(F_\{n0\}\) used to compute the critical force
depends on the form of the contact model. For non-cohesive models
({hertz}, {hertz/material}, {hooke}), it is given by the magnitude of
the normal force:
\begin\{equation\}
F_\{n0\} = \|\mathbf\{F\}_n\|
\end\{equation\}
For cohesive models such as {jkr} and {dmt}, the critical force is
adjusted so that the critical tangential force approaches \(\mu_t
F_\{pulloff\}\), see "Marshall"_#Marshall2009, equation 43, and
"Thornton"_#Thornton1991. For both models, \(F_\{n0\}\) takes the
form:
\begin\{equation\}
F_\{n0\} = \|\mathbf\{F\}_ne + 2 F_\{pulloff\}\|
\end\{equation\}
Where \(F_\{pulloff\} = 3\pi \gamma R \) for {jkr}, and
\(F_\{pulloff\} = 4\pi \gamma R \) for {dmt}.
The remaining tangential options all use accumulated tangential
displacement (i.e. contact history). This is discussed below in the
context of the {linear_history} option, but the same treatment of the
accumulated displacement applies to the other options as well.
For {tangential linear_history}, the tangential force is given by:
\begin\{equation\}
\mathbf\{F\}_t = -min(\mu_t F_\{n0\}, \|-k_t\mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
\end\{equation\}
Here, \(\mathbf\{\xi\}\) is the tangential displacement accumulated
during the entire duration of the contact:
\begin\{equation\}
\mathbf\{\xi\} = \int_\{t0\}^t \mathbf\{v\}_\{t,rel\}(\tau) \mathrm\{d\}\tau
\end\{equation\}
This accumulated tangential displacement must be adjusted to account
for changes in the frame of reference of the contacting pair of
particles during contact. This occurs due to the overall motion of the
contacting particles in a rigid-body-like fashion during the duration
of the contact. There are two modes of motion that are relevant: the
'tumbling' rotation of the contacting pair, which changes the
orientation of the plane in which tangential displacement occurs; and
'spinning' rotation of the contacting pair about the vector connecting
their centers of mass (\(\mathbf\{n\}\)). Corrections due to the
former mode of motion are made by rotating the accumulated
displacement into the plane that is tangential to the contact vector
at each step, or equivalently removing any component of the tangential
displacement that lies along \(\mathbf\{n\}\), and rescaling to
preserve the magnitude. This follows the discussion in
"Luding"_#Luding2008, see equation 17 and relevant discussion in that
work:
\begin\{equation\}
\mathbf\{\xi\} = \left(\mathbf\{\xi'\} - (\mathbf\{n\} \cdot \mathbf\{\xi'\})\mathbf\{n\}\right) \frac\{\|\mathbf\{\xi'\}\|\}\{\|\mathbf\{\xi'\}\| - \mathbf\{n\}\cdot\mathbf\{\xi'\}\}
\label\{eq:rotate_displacements\}
\end\{equation\}
Here, \(\mathbf\{\xi'\}\) is the accumulated displacement prior to the
current time step and \(\mathbf\{\xi\}\) is the corrected
displacement. Corrections to the displacement due to the second mode
of motion described above (rotations about \(\mathbf\{n\}\)) are not
currently implemented, but are expected to be minor for most
simulations.
Furthermore, when the tangential force exceeds the critical force, the
tangential displacement is re-scaled to match the value for the
critical force (see "Luding"_#Luding2008, equation 20 and related
discussion):
\begin\{equation\}
\mathbf\{\xi\} = -\frac\{1\}\{k_t\}\left(\mu_t F_\{n0\}\mathbf\{t\} + \mathbf\{F\}_\{t,damp\}\right)
\end\{equation\}
The tangential force is added to the total normal force (elastic plus
damping) to produce the total force on the particle. The tangential
force also acts at the contact point (defined as the center of the
overlap region) to induce a torque on each particle according to:
\begin\{equation\}
\mathbf\{\tau\}_i = -(R_i - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
\end\{equation\}
\begin\{equation\}
\mathbf\{\tau\}_j = -(R_j - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
\end\{equation\}
For {tangential mindlin}, the "Mindlin"_#Mindlin1949 no-slip solution is used, which differs from the {linear_history}
option by an additional factor of {a}, the radius of the contact region. The tangential force is given by:
\begin\{equation\}
\mathbf\{F\}_t = -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
\end\{equation\}
Here, {a} is the radius of the contact region, given by \(a = \delta
R\) for all normal contact models, except for {jkr}, where it is given
implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see
discussion above. To match the Mindlin solution, one should set \(k_t
= 8G\), where \(G\) is the shear modulus, related to Young's modulus
\(E\) by \(G = E/(2(1+\nu))\), where \(\nu\) is Poisson's ratio. This
can also be achieved by specifying {NULL} for \(k_t\), in which case a
normal contact model that specifies material parameters \(E\) and
\(\nu\) is required (e.g. {hertz/material}, {dmt} or {jkr}). In this
case, mixing of the shear modulus for different particle types {i} and
{j} is done according to:
\begin\{equation\}
1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j
\end\{equation\}
The {mindlin_rescale} option uses the same form as {mindlin}, but the
magnitude of the tangential displacement is re-scaled as the contact
unloads, i.e. if \(a < a_\{t_\{n-1\}\}\):
\begin\{equation\}
\mathbf\{\xi\} = \mathbf\{\xi_\{t_\{n-1\}\}\} \frac\{a\}\{a_\{t_\{n-1\}\}\}
\end\{equation\}
Here, \(t_\{n-1\}\) indicates the value at the previous time
step. This rescaling accounts for the fact that a decrease in the
contact area upon unloading leads to the contact being unable to
support the previous tangential loading, and spurious energy is
created without the rescaling above ("Walton"_#WaltonPC ). See also
discussion in "Thornton et al, 2013"_#Thornton2013 , particularly
equation 18(b) of that work and associated discussion.
:line
The optional {rolling} keyword enables rolling friction, which resists
pure rolling motion of particles. The options currently supported are:
{none}
{sds} : \(k_\{roll\}\), \(\gamma_\{roll\}\), \(\mu_\{roll\}\) :ol
If the {rolling} keyword is not specified, the model defaults to {none}.
For {rolling sds}, rolling friction is computed via a
spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed
by "Luding"_#Luding2008. Unlike the formulation in
"Marshall"_#Marshall2009, this allows for the required adjustment of
rolling displacement due to changes in the frame of reference of the
contacting pair. The rolling pseudo-force is computed analogously to
the tangential force:
\begin\{equation\}
\mathbf\{F\}_\{roll,0\} = k_\{roll\} \mathbf\{\xi\}_\{roll\} - \gamma_\{roll\} \mathbf\{v\}_\{roll\}
\end\{equation\}
Here, \(\mathbf\{v\}_\{roll\} = -R(\mathbf\{\Omega\}_i -
\mathbf\{\Omega\}_j) \times \mathbf\{n\}\) is the relative rolling
velocity, as given in "Wang et al"_#Wang2015 and
"Luding"_#Luding2008. This differs from the expressions given by "Kuhn
and Bagi"_#Kuhn2004 and used in "Marshall"_#Marshall2009; see "Wang et
al"_#Wang2015 for details. The rolling displacement is given by:
\begin\{equation\}
\mathbf\{\xi\}_\{roll\} = \int_\{t_0\}^t \mathbf\{v\}_\{roll\} (\tau) \mathrm\{d\} \tau
\end\{equation\}
A Coulomb friction criterion truncates the rolling pseudo-force if it
exceeds a critical value:
\begin\{equation\}
\mathbf\{F\}_\{roll\} = min(\mu_\{roll\} F_\{n,0\}, \|\mathbf\{F\}_\{roll,0\}\|)\mathbf\{k\}
\end\{equation\}
Here, \(\mathbf\{k\} =
\mathbf\{v\}_\{roll\}/\|\mathbf\{v\}_\{roll\}\|\) is the direction of
the pseudo-force. As with tangential displacement, the rolling
displacement is rescaled when the critical force is exceeded, so that
the spring length corresponds the critical force. Additionally, the
displacement is adjusted to account for rotations of the frame of
reference of the two contacting particles in a manner analogous to the
tangential displacement.
The rolling pseudo-force does not contribute to the total force on
either particle (hence 'pseudo'), but acts only to induce an equal and
opposite torque on each particle, according to:
\begin\{equation\}
\tau_\{roll,i\} = R_\{eff\} \mathbf\{n\} \times \mathbf\{F\}_\{roll\}
\end\{equation\}
\begin\{equation\}
\tau_\{roll,j\} = -\tau_\{roll,i\}
\end\{equation\}
:line
The optional {twisting} keyword enables twisting friction, which
resists rotation of two contacting particles about the vector
\(\mathbf\{n\}\) that connects their centers. The options currently
supported are:
{none}
{sds} : \(k_\{twist\}\), \(\gamma_\{twist\}\), \(\mu_\{twist\}\)
{marshall} :ol
If the {twisting} keyword is not specified, the model defaults to {none}.
For both {twisting sds} and {twisting marshall}, a history-dependent
spring-dashpot-slider is used to compute the twisting torque. Because
twisting displacement is a scalar, there is no need to adjust for
changes in the frame of reference due to rotations of the particle
pair. The formulation in "Marshall"_#Marshall2009 therefore provides
the most straightforward treatment:
\begin\{equation\}
\tau_\{twist,0\} = -k_\{twist\}\xi_\{twist\} - \gamma_\{twist\}\Omega_\{twist\}
\end\{equation\}
Here \(\xi_\{twist\} = \int_\{t_0\}^t \Omega_\{twist\} (\tau)
\mathrm\{d\}\tau\) is the twisting angular displacement, and
\(\Omega_\{twist\} = (\mathbf\{\Omega\}_i - \mathbf\{\Omega\}_j) \cdot
\mathbf\{n\}\) is the relative twisting angular velocity. The torque
is then truncated according to:
\begin\{equation\}
\tau_\{twist\} = min(\mu_\{twist\} F_\{n,0\}, \tau_\{twist,0\})
\end\{equation\}
Similar to the sliding and rolling displacement, the angular
displacement is rescaled so that it corresponds to the critical value
if the twisting torque exceeds this critical value:
\begin\{equation\}
\xi_\{twist\} = \frac\{1\}\{k_\{twist\}\} (\mu_\{twist\} F_\{n,0\}sgn(\Omega_\{twist\}) - \gamma_\{twist\}\Omega_\{twist\})
\end\{equation\}
For {twisting sds}, the coefficients \(k_\{twist\}, \gamma_\{twist\}\)
and \(\mu_\{twist\}\) are simply the user input parameters that follow
the {twisting sds} keywords in the {pair_coeff} command.
For {twisting_marshall}, the coefficients are expressed in terms of
sliding friction coefficients, as discussed in
"Marshall"_#Marshall2009 (see equations 32 and 33 of that work):
\begin\{equation\}
k_\{twist\} = 0.5k_ta^2
\end\{equation\}
\begin\{equation\}
\eta_\{twist\} = 0.5\eta_ta^2
\end\{equation\}
\begin\{equation\}
\mu_\{twist\} = \frac\{2\}\{3\}a\mu_t
\end\{equation\}
Finally, the twisting torque on each particle is given by:
\begin\{equation\}
\mathbf\{\tau\}_\{twist,i\} = \tau_\{twist\}\mathbf\{n\}
\end\{equation\}
\begin\{equation\}
\mathbf\{\tau\}_\{twist,j\} = -\mathbf\{\tau\}_\{twist,i\}
\end\{equation\}
:line
LAMMPS automatically sets pairwise cutoff values for {pair_style
granular} based on particle radii (and in the case of {jkr} pull-off
distances). In the vast majority of situations, this is adequate.
However, a cutoff value can optionally be appended to the {pair_style
granular} command to specify a global cutoff (i.e. a cutoff for all
atom types). Additionally, the optional {cutoff} keyword can be passed
to the {pair_coeff} command, followed by a cutoff value. This will
set a pairwise cutoff for the atom types in the {pair_coeff} command.
These options may be useful in some rare cases where the automatic
cutoff determination is not sufficient, e.g. if particle diameters
are being modified via the {fix adapt} command. In that case, the
global cutoff specified as part of the {pair_style granular} command
is applied to all atom types, unless it is overridden for a given atom
type combination by the {cutoff} value specified in the {pair coeff}
command. If {cutoff} is only specified in the {pair coeff} command
and no global cutoff is appended to the {pair_style granular} command,
then LAMMPS will use that cutoff for the specified atom type
combination, and automatically set pairwise cutoffs for the remaining
atom types.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
The "pair_modify"_pair_modify.html mix, shift, table, and tail options
are not relevant for granular pair styles.
Mixing of coefficients is carried out using geometric averaging for
most quantities, e.g. if friction coefficient for type 1-type 1
interactions is set to \(\mu_1\), and friction coefficient for type
2-type 2 interactions is set to \(\mu_2\), the friction coefficient
for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\)
(unless explicitly specified to a different value by a {pair_coeff 1 2
...} command. The exception to this is elastic modulus, only
applicable to {hertz/material}, {dmt} and {jkr} normal contact
models. In that case, the effective elastic modulus is computed as:
\begin\{equation\}
E_\{eff,ij\} = \left(\frac\{1-\nu_i^2\}\{E_i\} + \frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}
\end\{equation\}
If the {i-j} coefficients \(E_\{ij\}\) and \(\nu_\{ij\}\) are
explicitly specified, the effective modulus is computed as:
\begin\{equation\}
E_\{eff,ij\} = \left(\frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\} + \frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\}\right)^\{-1\}
\end\{equation\}
or
\begin\{equation\}
E_\{eff,ij\} = \frac\{E_\{ij\}\}\{2(1-\nu_\{ij\})\}
\end\{equation\}
These pair styles write their information to "binary restart
files"_restart.html, so a pair_style command does 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
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the pairwise interaction force. However, the single() function also
calculates 10 extra pairwise quantities. The first 3 are the
components of the tangential force between particles I and J, acting
on particle I. The 4th is the magnitude of this tangential force.
The next 3 (5-7) are the components of the rolling torque acting on
particle I. The next entry (8) is the magnitude of the rolling torque.
The next entry (9) is the magnitude of the twisting torque acting
about the vector connecting the two particle centers.
The last 3 (10-12) are the components of the vector connecting
the centers of the two particles (x_I - x_J).
These extra quantities can be accessed by the "compute
pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
{p12}.
:line
[Restrictions:]
All the granular pair styles are part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
require a per-particle radius is stored. The {sphere} atom style does
all of this.
This pair style requires you to use the "comm_modify vel
yes"_comm_modify.html command so that velocities are stored by ghost
atoms.
These pair styles will not restart exactly when using the
"read_restart"_read_restart.html command, though they should provide
statistically similar results. This is because the forces they
compute depend on atom velocities. See the
"read_restart"_read_restart.html command for more details.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair gran/*"_pair_gran.html
[Default:]
For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
{twisting none}.
[References:]
:link(Brill1996)
[(Brilliantov et al, 1996)] Brilliantov, N. V., Spahn, F., Hertzsch,
J. M., & Poschel, T. (1996). Model for collisions in granular
gases. Physical review E, 53(5), 5382.
:link(Tsuji1992)
[(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
T. (1992). Lagrangian numerical simulation of plug flow of
cohesionless particles in a horizontal pipe. Powder technology, 71(3),
239-250.
:link(JKR1971)
[(Johnson et al, 1971)] Johnson, K. L., Kendall, K., & Roberts,
A. D. (1971). Surface energy and the contact of elastic
solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
:link(DMT1975)
[Derjaguin et al, 1975)] Derjaguin, B. V., Muller, V. M., & Toporov,
Y. P. (1975). Effect of contact deformations on the adhesion of
particles. Journal of Colloid and interface science, 53(2), 314-326.
:link(Luding2008)
[(Luding, 2008)] Luding, S. (2008). Cohesive, frictional powders:
contact models for tension. Granular matter, 10(4), 235.
:link(Marshall2009)
[(Marshall, 2009)] Marshall, J. S. (2009). Discrete-element modeling
of particulate aerosol flows. Journal of Computational Physics,
228(5), 1541-1561.
:link(Silbert2001)
[(Silbert, 2001)] Silbert, L. E., Ertas, D., Grest, G. S., Halsey,
T. C., Levine, D., & Plimpton, S. J. (2001). Granular flow down an
inclined plane: Bagnold scaling and rheology. Physical Review E,
64(5), 051302.
:link(Kuhn2004)
[(Kuhn and Bagi, 2005)] Kuhn, M. R., & Bagi, K. (2004). Contact
rolling and deformation in granular media. International journal of
solids and structures, 41(21), 5793-5820.
:link(Wang2015)
[(Wang et al, 2015)] Wang, Y., Alonso-Marroquin, F., & Guo,
W. W. (2015). Rolling and sliding in 3-D discrete element
models. Particuology, 23, 49-55.
:link(Thornton1991)
[(Thornton, 1991)] Thornton, C. (1991). Interparticle sliding in the
presence of adhesion. J. Phys. D: Appl. Phys. 24 1942
:link(Mindlin1949)
[(Mindlin, 1949)] Mindlin, R. D. (1949). Compliance of elastic bodies
in contact. J. Appl. Mech., ASME 16, 259-268.
:link(Thornton2013)
[(Thornton et al, 2013)] Thornton, C., Cummins, S. J., & Cleary,
P. W. (2013). An investigation of the comparative behaviour of
alternative contact force models during inelastic collisions. Powder
Technology, 233, 30-46.
:link(WaltonPC)
[(Otis R. Walton)] Walton, O.R., Personal Communication

19
doc/src/pair_ilp_graphene_hbn.txt
View File

@ -47,11 +47,16 @@ equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
NOTE: This potential is intended for interactions between two different
layers of graphene or hexagonal boron nitride. Therefore, to avoid
interaction within the same layers, each layer should have a separate
molecule id and is recommended to use "full" atom style in the data
file.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
To perform a realistic simulation, this potential must be used in combination with
intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
The parameter file (e.g. BNCH.ILP), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters,
@ -62,6 +67,10 @@ 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.
The parameters for atoms pairs between Boron and Nitrogen are fitted with
a screened Coulomb interaction "coul/shield"_pair_coul_shield.html. Therefore,
to simulated the properties of h-BN correctly, this potential must be used in
combination with the pair style "coul/shield"_pair_coul_shield.html.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide

7
doc/src/pair_kim.txt
View File

@ -42,11 +42,8 @@ section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
See the examples/kim dir for an input script that uses a KIM model (potential)
for Lennard-Jones. Note, for this example input script, the example models
shipped with with kim-api package must be installed. See the "Build
package"_Build_package.html section and the ./lib/kim/README for details
on how to build LAMMSPS with the kim-api and how to install the example models.
See the examples/kim dir for an input script that uses a KIM model
(potential) for Lennard-Jones.
:line

14
doc/src/pair_kolmogorov_crespi_full.txt
View File

@ -42,10 +42,16 @@ the last term in the equation for {Vij} above. This is essential only
when the tapper function is turned off. The formula of taper function
can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential is intended for interactions between two different
graphene layers. Therefore, to avoid interaction within the same layers,
each layer should have a separate molecule id and is recommended to use
"full" atom style in the data file.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene. To perform a realistic simulation, this potential
must be used in combination with intra-layer potential, such as
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
The parameter file (e.g. CH.KC), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters, {S},

7
doc/src/pair_meamc.txt
View File

@ -357,6 +357,13 @@ The {meam/c} style is provided in the USER-MEAMC package. It is
only enabled if LAMMPS was built with that package.
See the "Build package"_Build_package.html doc page for more info.
The maximum number of elements, that can be read from the MEAM
library file, is determined at compile time. The default is 5.
If you need support for more elements, you have to change the
define for the constant 'maxelt' at the beginning of the file
src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
limit on the number of atoms types.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,

1
doc/src/pairs.txt
View File

@ -42,6 +42,7 @@ Pair Styles :h1
pair_gauss
pair_gayberne
pair_gran
pair_granular
pair_gromacs
pair_gw
pair_hbond_dreiding

2
doc/src/velocity.txt
View File

@ -134,7 +134,7 @@ The {mom} and {rot} keywords are used by {create}. If mom = yes, the
linear momentum of the newly created ensemble of velocities is zeroed;
if rot = yes, the angular momentum is zeroed.
*line
:line
If specified, the {temp} keyword is used by {create} and {scale} to
specify a "compute"_compute.html that calculates temperature in a

36
doc/utils/sphinx-config/false_positives.txt
View File

@ -156,6 +156,8 @@ ba
Babadi
backcolor
Baczewski
Bagi
Bagnold
Bal
balancer
Balankura
@ -250,6 +252,7 @@ Boresch
Botero
Botu
Bouguet
Bourne
boxcolor
bp
bpls
@ -286,6 +289,7 @@ Cao
Capolungo
Caro
cartesian
CasP
Caswell
Cates
Cavium
@ -345,7 +349,9 @@ Cii
Cij
cis
civ
Clang
clearstore
Cleary
Clebsch
clemson
Clermont
@ -372,6 +378,7 @@ Coeff
CoefficientN
coeffs
Coeffs
cohesionless
Coker
Colberg
coleman
@ -449,6 +456,7 @@ cuda
Cuda
CUDA
CuH
Cummins
Curk
customIDs
cutbond
@ -492,6 +500,7 @@ darkturquoise
darkviolet
Das
Dasgupta
dashpot
dat
datafile
datums
@ -529,6 +538,7 @@ Dequidt
der
derekt
Derjagin
Derjaguin
Derlet
Deserno
Destree
@ -627,6 +637,7 @@ dVx
dW
dx
dy
dylib
dyn
dyne
dynes
@ -647,6 +658,7 @@ ec
Ec
ecoul
ecp
Ecut
edgeIDs
edihed
edim
@ -1079,6 +1091,7 @@ Hyoungki
hyperdynamics
hyperradius
hyperspherical
hysteretic
Ibanez
ibar
ibm
@ -1124,6 +1137,7 @@ infty
inhomogeneities
inhomogeneous
init
initio
initializations
InP
inregion
@ -1138,6 +1152,7 @@ interconvert
interial
interlayer
intermolecular
Interparticle
interstitials
Intr
intra
@ -1156,6 +1171,7 @@ IPython
Isele
isenthalpic
ish
Ishida
iso
isodemic
isoenergetic
@ -1243,6 +1259,7 @@ Jy
Jz
jzimmer
Kadiri
Kai
Kalia
Kamberaj
Kapfer
@ -1265,6 +1282,7 @@ kcl
Kd
KDevelop
ke
kepler
KE
Keblinski
keflag
@ -1272,6 +1290,7 @@ Keir
Kelchner
Kelkar
Kemper
keV
Keyes
Khersonskii
Khrapak
@ -1298,6 +1317,7 @@ Kondor
konglt
Koning
Kooser
Korn
Koskinen
Koster
Kosztin
@ -1382,6 +1402,7 @@ libAtoms
libawpmd
libch
libcolvars
libcurl
libdir
libdl
libfftw
@ -1449,6 +1470,7 @@ logfile
logfreq
logicals
Lomdahl
Lond
lookups
Lookups
LoopVar
@ -1464,6 +1486,7 @@ lsfftw
ltbbmalloc
lubricateU
lucy
Luding
Lussetti
Lustig
lwsock
@ -1502,6 +1525,7 @@ manybody
MANYBODY
Maras
Marrink
Marroquin
Marsaglia
Marseille
Martyna
@ -1513,12 +1537,14 @@ masstotal
Masuhiro
Matchett
Materias
mathbf
matlab
matplotlib
Mattox
Mattson
maxangle
maxbond
maxelt
maxeval
maxfiles
Maxfoo
@ -1601,12 +1627,14 @@ Mie
Mikami
Militzer
Minary
Mindlin
mincap
mingw
minima
minimizations
minimizer
minimizers
minneigh
minorder
minSteps
mintcream
@ -1671,6 +1699,7 @@ mpiexec
mpiio
mpirun
mplayer
mps
Mryglod
mscg
MSCG
@ -1954,6 +1983,7 @@ oneway
onn
ons
OO
opencl
openKIM
OpenMP
openmp
@ -2286,6 +2316,7 @@ rg
Rg
Rhaphson
rheological
rheology
rhodo
Rhodo
rhodopsin
@ -2602,6 +2633,7 @@ Tait
taitwater
Tajkhorshid
Tamaskovics
Tanaka
tanh
Tartakovsky
taskset
@ -2689,6 +2721,7 @@ tokyo
tol
toolchain
topologies
Toporov
Torder
torsions
Tosi
@ -2733,6 +2766,7 @@ Tsrd
Tstart
tstat
Tstop
Tsuji
Tsuzuki
tt
Tt
@ -2783,6 +2817,7 @@ unimodal
unitless
Universite
unix
unmaintained
unoptimized
unpadded
unphysical
@ -2918,6 +2953,7 @@ Wi
Wicaksono
wih
Wijk
Wikipedia
wildcard
Wildcard
Wirnsberger

55
examples/SPIN/spinmin/in.spinmin.bfo Normal file
View File

@ -0,0 +1,55 @@
# bfo in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
region box block 0.0 34.0 0.0 34.0 0.0 1.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 1.0
set group all spin/random 11 2.50
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
#pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 50
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin
min_modify alpha_damp 1.0 discrete_factor 10.0
minimize 1.0e-10 0.0 1000 100

55
examples/SPIN/spinmin/in.spinmin.iron Normal file
View File

@ -0,0 +1,55 @@
# bcc iron in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice bcc 2.8665
region box block 0.0 4.0 0.0 4.0 0.0 4.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 55.845
set group all spin/random 31 2.2
#set group all spin 2.2 1.0 1.0 -1.0
pair_style spin/exchange 3.5
pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
fix 1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 100
thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin
min_modify alpha_damp 1.0 discrete_factor 10.0
minimize 1.0e-10 1.0e-10 100000 1000

14
examples/USER/misc/electron_stopping/Si.Si.elstop Normal file
View File

@ -0,0 +1,14 @@
# Electronic stopping for Si in Si
# Uses metal units
# Kinetic energy in eV, stopping power in eV/A
# For other atom types, add columns.
# energy Si in Si
3918.2 6.541
15672.9 13.091
35263.9 19.660
62691.5 26.257
97955.4 32.889
141055.9 39.566
191992.0 46.292
250766.1 53.074

1
examples/USER/misc/electron_stopping/Si.sw Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/Si.sw

38
examples/USER/misc/electron_stopping/in.elstop Normal file
View File

@ -0,0 +1,38 @@
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 5.431
region rbox block -10 10 -10 10 -10 10
create_box 1 rbox
mass 1 28.0855
create_atoms 1 box
velocity all create 300 42534 mom yes rot yes
group gPKA id 1
velocity gPKA set 1120 1620 389
pair_style sw
pair_coeff * * Si.sw Si
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10
thermo_style custom step time dt f_fel
#compute ek all ke/atom
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
run 5000

39
examples/USER/misc/electron_stopping/in.elstop.only Normal file
View File

@ -0,0 +1,39 @@
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 1
region rbox block -100 100 -100 100 -100 100
region rsmallbox block -90 90 -90 90 -90 90
create_box 1 rbox
mass 1 28.0855
create_atoms 1 single 0 0 0
velocity all set 1120 1620 389
pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom
compute ektot all reduce sum c_ek
thermo 100
thermo_style custom step time dt f_fel c_ektot
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
run 10000

597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1 Normal file
View File

@ -0,0 +1,597 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region rbox block -10 10 -10 10 -10 10
create_box 1 rbox
Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
1 by 1 by 1 MPI processor grid
mass 1 28.0855
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00282311 secs
velocity all create 300 42534 mom yes rot yes
group gPKA id 1
1 atoms in group gPKA
velocity gPKA set 1120 1620 389
pair_style sw
pair_coeff * * Si.sw Si
Reading potential file Si.sw with DATE: 2007-06-11
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10
thermo_style custom step time dt f_fel
#compute ek all ke/atom
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.77118
ghost atom cutoff = 5.77118
binsize = 2.88559, bins = 38 38 38
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) fix electron/stopping, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
Step Time Dt f_fel
0 0 4.98128e-05 0
10 0.00030141297 7.4132113e-06 143.83504
20 0.00035951427 6.0316944e-06 171.53673
30 0.00057458971 3.5117251e-05 274.07596
40 0.00086591312 5.8243334e-06 412.87446
50 0.00090045701 2.1026443e-06 429.31458
60 0.00091828462 1.5368285e-06 437.79421
70 0.00093305888 1.4643253e-06 444.81982
80 0.00094860749 1.7487528e-06 452.21378
90 0.00097032161 3.0786693e-06 462.54244
100 0.0010787914 4.9354535e-05 514.16832
110 0.0012080771 2.321306e-06 575.68374
120 0.0012239682 1.0510328e-06 583.23471
130 0.0012325497 6.8272619e-07 587.30872
140 0.0012385196 5.1205819e-07 590.14077
150 0.001243165 4.1524338e-07 592.34294
160 0.0012470201 3.5380824e-07 594.1694
170 0.0012503578 3.1203776e-07 595.74992
180 0.0012533367 2.8236408e-07 597.15986
190 0.0012560575 2.6071908e-07 598.44711
200 0.0012585888 2.4474123e-07 599.64431
210 0.0012609803 2.3298466e-07 600.77504
220 0.0012632696 2.2453464e-07 601.85726
230 0.0012654871 2.1880713e-07 602.90531
240 0.0012676582 2.1543942e-07 603.93128
250 0.0012698054 2.1422997e-07 604.94591
260 0.0012719499 2.1510772e-07 605.95925
270 0.0012741128 2.1812163e-07 606.98126
280 0.0012763159 2.2344765e-07 608.02243
290 0.0012785839 2.3141489e-07 609.09436
300 0.0012809453 2.425587e-07 610.21066
310 0.0012834353 2.577174e-07 611.38806
320 0.0012860996 2.7820843e-07 612.64822
330 0.0012890001 3.0616141e-07 614.02061
340 0.0012922261 3.4518994e-07 615.54764
350 0.0012959145 4.0187423e-07 617.29438
360 0.0013002933 4.894618e-07 619.36917
370 0.0013057872 6.3886828e-07 621.97388
380 0.0013133355 9.4153332e-07 625.55502
390 0.0013257779 1.8246429e-06 631.46263
400 0.0013651328 1.4820738e-05 650.16503
410 0.0016916358 4.5528312e-05 805.3327
420 0.0020836696 2.6189823e-05 991.45963
430 0.002192113 5.1312984e-06 1042.8979
440 0.0022530638 1.1643276e-05 1071.7967
450 0.0025312898 1.5833134e-05 1203.6961
460 0.0028677695 3.9078523e-05 1363.0792
470 0.0032653301 3.9299497e-05 1551.2027
480 0.0036647478 4.1100578e-05 1739.9906
490 0.0040772194 3.6017871e-05 1934.7262
500 0.004246426 1.1620229e-05 2014.5366
510 0.0045410379 2.1151987e-05 2153.4172
520 0.0048951987 4.2067206e-05 2320.2216
530 0.0051251181 5.9152255e-06 2428.4156
540 0.0051740847 5.0188036e-06 2451.4388
550 0.0053207575 4.1618335e-05 2520.4067
560 0.0054412772 2.3641932e-06 2577.0541
570 0.005457552 1.0847369e-06 2584.6937
580 0.0054664476 7.1198746e-07 2588.8658
590 0.0054726999 5.3933302e-07 2591.796
600 0.0054776139 4.4178461e-07 2594.0976
610 0.0054817341 3.8039473e-07 2596.0263
620 0.0054853401 3.3924667e-07 2597.7135
630 0.0054885957 3.1069211e-07 2599.2361
640 0.0054916066 2.9064829e-07 2600.6439
650 0.0054944462 2.7678405e-07 2601.9712
660 0.0054971697 2.6772348e-07 2603.244
670 0.0054998211 2.6266505e-07 2604.4829
680 0.0055024383 2.6119265e-07 2605.7058
690 0.0055050563 2.6318733e-07 2606.929
700 0.0055077103 2.6880326e-07 2608.1691
710 0.0055104383 2.7849814e-07 2609.4439
720 0.0055132846 2.9313007e-07 2610.7742
730 0.0055163044 3.141612e-07 2612.186
740 0.0055195719 3.4406726e-07 2613.714
750 0.0055231932 3.8719688e-07 2615.4081
760 0.0055273329 4.5174267e-07 2617.3455
770 0.0055322712 5.5490406e-07 2619.6579
780 0.0055385515 7.3934538e-07 2622.6004
790 0.0055474645 1.1452909e-06 2626.7792
800 0.0055635927 2.6160295e-06 2634.3465
810 0.0057044835 3.9642931e-05 2700.5132
820 0.0060307501 2.9394558e-05 2853.6539
830 0.0063374404 8.5188148e-06 2997.4768
840 0.0063740052 1.4828325e-06 3014.6052
850 0.0063848364 7.5985425e-07 3019.6727
860 0.0063911095 5.0258852e-07 3022.6045
870 0.0063954921 3.7335256e-07 3024.6508
880 0.0063988506 2.9643864e-07 3026.2175
890 0.0064015712 2.4575869e-07 3027.4855
900 0.0064038584 2.1001191e-07 3028.5506
910 0.0064058333 1.8353805e-07 3029.4694
920 0.006407573 1.6320008e-07 3030.2782
930 0.0064091297 1.4712417e-07 3031.0014
940 0.0064105403 1.3412445e-07 3031.6562
950 0.0064118317 1.2341509e-07 3032.2552
960 0.0064130243 1.1445544e-07 3032.808
970 0.0064141337 1.0686175e-07 3033.3219
980 0.0064151722 1.0035437e-07 3033.8027
990 0.0064161498 9.4724852e-08 3034.2549
1000 0.0064170744 8.9814769e-08 3034.6824
1010 0.0064179527 8.5501639e-08 3035.0882
1020 0.0064187902 8.1689338e-08 3035.475
1030 0.0064195915 7.8301418e-08 3035.8449
1040 0.0064203606 7.5276356e-08 3036.1997
1050 0.0064211009 7.2564109e-08 3036.541
1060 0.0064218154 7.0123584e-08 3036.8703
1070 0.0064225065 6.7920744e-08 3037.1886
1080 0.0064231766 6.5927178e-08 3037.4971
1090 0.0064238276 6.4119002e-08 3037.7967
1100 0.0064244613 6.2476011e-08 3038.0882
1110 0.0064250792 6.0981016e-08 3038.3724
1120 0.0064256828 5.9619315e-08 3038.6498
1130 0.0064262733 5.8378279e-08 3038.9212
1140 0.0064268519 5.7247013e-08 3039.1869
1150 0.0064274196 5.6216088e-08 3039.4476
1160 0.0064279775 5.5277318e-08 3039.7037
1170 0.0064285264 5.4423582e-08 3039.9556
1180 0.006429067 5.3648672e-08 3040.2036
1190 0.0064296003 5.294717e-08 3040.4482
1200 0.0064301269 5.2314351e-08 3040.6897
1210 0.0064306474 5.1746091e-08 3040.9283
1220 0.0064311625 5.1238802e-08 3041.1644
1230 0.0064316729 5.0789368e-08 3041.3983
1240 0.0064321789 5.0395101e-08 3041.6301
1250 0.0064326813 5.0053692e-08 3041.8603
1260 0.0064331805 4.9763183e-08 3042.0889
1270 0.006433677 4.9521937e-08 3042.3163
1280 0.0064341713 4.9328614e-08 3042.5427
1290 0.0064346639 4.9182151e-08 3042.7682
1300 0.0064351552 4.9081752e-08 3042.9931
1310 0.0064356458 4.9026872e-08 3043.2177
1320 0.006436136 4.9017214e-08 3043.4421
1330 0.0064366262 4.9052721e-08 3043.6666
1340 0.0064371171 4.9133581e-08 3043.8912
1350 0.006437609 4.9260223e-08 3044.1164
1360 0.0064381023 4.9433327e-08 3044.3422
1370 0.0064385976 4.9653831e-08 3044.569
1380 0.0064390953 4.9922944e-08 3044.7968
1390 0.0064395959 5.0242164e-08 3045.0261
1400 0.0064401 5.0613297e-08 3045.2568
1410 0.006440608 5.1038483e-08 3045.4895
1420 0.0064411205 5.1520228e-08 3045.7242
1430 0.0064416381 5.2061443e-08 3045.9613
1440 0.0064421614 5.2665486e-08 3046.201
1450 0.006442691 5.3336219e-08 3046.4437
1460 0.0064432276 5.4078074e-08 3046.6896
1470 0.006443772 5.4896126e-08 3046.9392
1480 0.0064443249 5.5796191e-08 3047.1927
1490 0.0064448873 5.6784937e-08 3047.4506
1500 0.0064454599 5.7870017e-08 3047.7132
1510 0.0064460439 5.9060235e-08 3047.9812
1520 0.0064466403 6.0365742e-08 3048.2549
1530 0.0064472503 6.1798287e-08 3048.5349
1540 0.0064478752 6.337151e-08 3048.822
1550 0.0064485166 6.5101323e-08 3049.1166
1560 0.006449176 6.7006371e-08 3049.4197
1570 0.0064498554 6.9108623e-08 3049.732
1580 0.0064505567 7.1434118e-08 3050.0546
1590 0.0064512824 7.4013931e-08 3050.3885
1600 0.0064520352 7.6885409e-08 3050.7351
1610 0.0064528182 8.0093813e-08 3051.0957
1620 0.006453635 8.3694486e-08 3051.472
1630 0.0064544898 8.7755778e-08 3051.8661
1640 0.0064553876 9.2363047e-08 3052.2802
1650 0.0064563343 9.7624226e-08 3052.7171
1660 0.0064573371 1.0367771e-07 3053.1801
1670 0.0064584046 1.1070379e-07 3053.6733
1680 0.0064595476 1.1894157e-07 3054.2017
1690 0.0064607796 1.2871484e-07 3054.7716
1700 0.0064621178 1.4047265e-07 3055.391
1710 0.0064635847 1.5485559e-07 3056.0705
1720 0.0064652106 1.7280864e-07 3056.8241
1730 0.0064670371 1.9578361e-07 3057.6713
1740 0.0064691241 2.261258e-07 3058.6401
1750 0.0064715615 2.6787347e-07 3059.7724
1760 0.0064744931 3.2858822e-07 3061.1353
1770 0.0064781697 4.2416554e-07 3062.8461
1780 0.0064830857 5.9426003e-07 3065.1356
1790 0.0064904338 9.7042692e-07 3068.5608
1800 0.006504521 2.3570057e-06 3075.1339
1810 0.0066489551 2.5350137e-05 3142.596
1820 0.0067263358 2.0982567e-06 3178.7218
1830 0.0067413263 1.0389873e-06 3185.7117
1840 0.0067499639 7.021379e-07 3189.736
1850 0.0067561793 5.4125252e-07 3192.6298
1860 0.00676114 4.4920623e-07 3194.938
1870 0.0067653505 3.911598e-07 3196.8961
1880 0.0067690759 3.5254253e-07 3198.6279
1890 0.0067724748 3.2626983e-07 3200.2074
1900 0.0067756518 3.0855768e-07 3201.6834
1910 0.0067786819 2.9728199e-07 3203.0908
1920 0.0067816236 2.9125633e-07 3204.457
1930 0.0067845263 2.8989566e-07 3205.8049
1940 0.0067874357 2.9306921e-07 3207.156
1950 0.0067903982 3.0106889e-07 3208.5318
1960 0.006793465 3.1467844e-07 3209.9563
1970 0.0067966982 3.3537556e-07 3211.4583
1980 0.0068001793 3.6577201e-07 3213.0759
1990 0.0068040239 4.1056728e-07 3214.863
2000 0.0068084116 4.7878365e-07 3216.9034
2010 0.0068136505 5.897605e-07 3219.3409
2020 0.0068203489 7.9292336e-07 3222.4591
2030 0.0068300039 1.259738e-06 3226.9568
2040 0.0068484332 3.1869606e-06 3235.5484
2050 0.00704302 3.1308435e-05 3326.3332
2060 0.0073582601 1.9393034e-05 3473.3099
2070 0.0076291992 6.1118973e-06 3599.5265
2080 0.0076591273 1.397136e-06 3613.4525
2090 0.0076695786 7.5324795e-07 3618.31
2100 0.0076758692 5.1095756e-07 3621.2308
2110 0.0076803593 3.8613872e-07 3623.3137
2120 0.0076838539 3.1077232e-07 3624.9334
2130 0.0076867208 2.6065521e-07 3626.2611
2140 0.0076891581 2.2509342e-07 3627.3889
2150 0.007691284 1.9865679e-07 3628.372
2160 0.0076931748 1.7830513e-07 3629.2457
2170 0.0076948825 1.6220815e-07 3630.0343
2180 0.0076964439 1.4920028e-07 3630.7548
2190 0.0076978861 1.3850522e-07 3631.42
2200 0.0076992297 1.2958672e-07 3632.0393
2210 0.0077004907 1.2206289e-07 3632.6203
2220 0.0077016817 1.1565477e-07 3633.1687
2230 0.0077028128 1.1015407e-07 3633.6892
2240 0.0077038924 1.0540234e-07 3634.1859
2250 0.0077049274 1.0127711e-07 3634.6618
2260 0.0077059236 9.7682361e-08 3635.1197
2270 0.0077068859 9.454193e-08 3635.5619
2280 0.0077078187 9.1794781e-08 3635.9903
2290 0.0077087255 8.9391579e-08 3636.4067
2300 0.0077096098 8.7292175e-08 3636.8125
2310 0.0077104742 8.5463727e-08 3637.2092
2320 0.0077113216 8.3879281e-08 3637.598
2330 0.007712154 8.2516693e-08 3637.9798
2340 0.0077129738 8.1357804e-08 3638.3557
2350 0.0077137829 8.0387796e-08 3638.7267
2360 0.0077145831 7.9594705e-08 3639.0935
2370 0.0077153761 7.8969036e-08 3639.457
2380 0.0077161635 7.8503481e-08 3639.8178
2390 0.007716947 7.8192701e-08 3640.1769
2400 0.0077177281 7.8033171e-08 3640.5348
2410 0.0077185083 7.8023089e-08 3640.8923
2420 0.007719289 7.8162318e-08 3641.25
2430 0.0077200718 7.8452384e-08 3641.6087
2440 0.0077208582 7.8896522e-08 3641.9691
2450 0.0077216498 7.9499759e-08 3642.3318
2460 0.0077224481 8.026906e-08 3642.6977
2470 0.0077232549 8.1213529e-08 3643.0675
2480 0.0077240719 8.2344683e-08 3643.442
2490 0.0077249012 8.3676812e-08 3643.8222
2500 0.0077257448 8.5227445e-08 3644.209
2510 0.0077266049 8.7017961e-08 3644.6035
2520 0.0077274841 8.9074372e-08 3645.0068
2530 0.0077283852 9.1428349e-08 3645.4203
2540 0.0077293113 9.4118559e-08 3645.8454
2550 0.0077302659 9.7192441e-08 3646.2837
2560 0.0077312533 1.0070857e-07 3646.7372
2570 0.0077322781 1.0473987e-07 3647.208
2580 0.0077333458 1.0937801e-07 3647.6987
2590 0.007734463 1.1473957e-07 3648.2124
2600 0.0077356377 1.2097481e-07 3648.7528
2610 0.0077368793 1.2828037e-07 3649.3242
2620 0.0077381998 1.3691837e-07 3649.9322
2630 0.0077396139 1.4724543e-07 3650.5836
2640 0.0077411406 1.5975888e-07 3651.2873
2650 0.0077428048 1.7517253e-07 3652.0548
2660 0.0077446398 1.9454711e-07 3652.9016
2670 0.0077466922 2.1952673e-07 3653.8493
2680 0.0077490288 2.5279733e-07 3654.929
2690 0.0077517515 2.9905194e-07 3656.188
2700 0.0077550252 3.6725589e-07 3657.7029
2710 0.0077591434 4.7681009e-07 3659.6101
2720 0.0077647038 6.7839241e-07 3662.1874
2730 0.007773234 1.1552111e-06 3666.1446
2740 0.0077911374 3.3406902e-06 3674.458
2750 0.0079702 8.4184292e-06 3757.6696
2760 0.008006114 1.4496754e-06 3774.3449
2770 0.0080166835 7.3926386e-07 3779.2462
2780 0.0080227734 4.8640717e-07 3782.0672
2790 0.0080270055 3.5945058e-07 3784.0255
2800 0.0080302318 2.8394384e-07 3785.517
2810 0.008032832 2.3422206e-07 3786.7179
2820 0.0080350072 1.9916814e-07 3787.7215
2830 0.0080368761 1.7321525e-07 3788.5831
2840 0.0080385144 1.5327931e-07 3789.3377
2850 0.0080399734 1.3751893e-07 3790.0091
2860 0.0080412891 1.2476931e-07 3790.6141
2870 0.0080424879 1.1425897e-07 3791.1649
2880 0.0080435897 1.0545738e-07 3791.6707
2890 0.0080446097 9.7988142e-08 3792.1386
2900 0.0080455599 9.1577084e-08 3792.5741
2910 0.00804645 8.6019912e-08 3792.9818
2920 0.0080472879 8.1161402e-08 3793.3653
2930 0.0080480798 7.6881575e-08 3793.7275
2940 0.0080488311 7.3086284e-08 3794.0709
2950 0.0080495465 6.9700651e-08 3794.3977
2960 0.0080502295 6.666441e-08 3794.7094
2970 0.0080508836 6.3928523e-08 3795.0078
2980 0.0080515116 6.1452701e-08 3795.2941
2990 0.0080521158 5.9203545e-08 3795.5694
3000 0.0080526985 5.7153146e-08 3795.8346
3010 0.0080532614 5.5278009e-08 3796.0908
3020 0.0080538063 5.3558217e-08 3796.3386
3030 0.0080543347 5.1976785e-08 3796.5788
3040 0.0080548478 5.051914e-08 3796.8119
3050 0.0080553469 4.9172716e-08 3797.0385
3060 0.0080558329 4.7926619e-08 3797.2591
3070 0.0080563069 4.6771366e-08 3797.4741
3080 0.0080567697 4.5698662e-08 3797.6839
3090 0.0080572222 4.4701228e-08 3797.8889
3100 0.0080576649 4.3772647e-08 3798.0895
3110 0.0080580987 4.2907247e-08 3798.2858
3120 0.0080585241 4.2099999e-08 3798.4784
3130 0.0080589417 4.1346425e-08 3798.6672
3140 0.0080593519 4.0642535e-08 3798.8527
3150 0.0080597554 3.9984758e-08 3799.0351
3160 0.0080601524 3.9369895e-08 3799.2145
3170 0.0080605435 3.8795073e-08 3799.3911
3180 0.008060929 3.8257705e-08 3799.5651
3190 0.0080613093 3.7755461e-08 3799.7368
3200 0.0080616847 3.7286239e-08 3799.9062
3210 0.0080620556 3.6848135e-08 3800.0734
3220 0.0080624222 3.6439432e-08 3800.2387
3230 0.0080627848 3.6058573e-08 3800.4022
3240 0.0080631438 3.5704146e-08 3800.564
3250 0.0080634994 3.5374876e-08 3800.7241
3260 0.0080638517 3.5069606e-08 3800.8828
3270 0.0080642011 3.4787289e-08 3801.0402
3280 0.0080645478 3.4526978e-08 3801.1962
3290 0.008064892 3.4287819e-08 3801.3511
3300 0.0080652339 3.4069042e-08 3801.505
3310 0.0080655736 3.3869955e-08 3801.6578
3320 0.0080659115 3.368994e-08 3801.8098
3330 0.0080662477 3.3528444e-08 3801.961
3340 0.0080665823 3.3384981e-08 3802.1115
3350 0.0080669156 3.3259123e-08 3802.2613
3360 0.0080672476 3.3150499e-08 3802.4106
3370 0.0080675787 3.305879e-08 3802.5594
3380 0.008067909 3.2983732e-08 3802.7078
3390 0.0080682385 3.2925108e-08 3802.8559
3400 0.0080685676 3.288275e-08 3803.0038
3410 0.0080688963 3.2856537e-08 3803.1515
3420 0.0080692248 3.2846395e-08 3803.2991
3430 0.0080695532 3.2852293e-08 3803.4466
3440 0.0080698819 3.2874247e-08 3803.5943
3450 0.0080702108 3.2912319e-08 3803.742
3460 0.0080705401 3.2966617e-08 3803.89
3470 0.0080708701 3.3037293e-08 3804.0382
3480 0.0080712008 3.312455e-08 3804.1868
3490 0.0080715325 3.3228638e-08 3804.3358
3500 0.0080718653 3.3349858e-08 3804.4853
3510 0.0080721995 3.3488567e-08 3804.6355
3520 0.008072535 3.3645172e-08 3804.7862
3530 0.0080728723 3.3820145e-08 3804.9378
3540 0.0080732113 3.4014016e-08 3805.0901
3550 0.0080735524 3.4227383e-08 3805.2434
3560 0.0080738957 3.4460914e-08 3805.3977
3570 0.0080742414 3.4715354e-08 3805.5532
3580 0.0080745898 3.4991532e-08 3805.7098
3590 0.0080749411 3.5290364e-08 3805.8677
3600 0.0080752954 3.5612865e-08 3806.0271
3610 0.0080756531 3.5960156e-08 3806.188
3620 0.0080760143 3.6333475e-08 3806.3505
3630 0.0080763794 3.6734187e-08 3806.5148
3640 0.0080767487 3.7163802e-08 3806.681
3650 0.0080771224 3.7623985e-08 3806.8492
3660 0.0080775008 3.8116577e-08 3807.0196
3670 0.0080778843 3.8643614e-08 3807.1924
3680 0.0080782733 3.9207349e-08 3807.3676
3690 0.008078668 3.9810283e-08 3807.5455
3700 0.008079069 4.0455191e-08 3807.7262
3710 0.0080794766 4.114516e-08 3807.91
3720 0.0080798913 4.1883634e-08 3808.0971
3730 0.0080803137 4.2674459e-08 3808.2877
3740 0.0080807442 4.3521941e-08 3808.482
3750 0.0080811834 4.4430917e-08 3808.6803
3760 0.0080816321 4.5406834e-08 3808.883
3770 0.0080820908 4.6455843e-08 3809.0902
3780 0.0080825604 4.7584918e-08 3809.3025
3790 0.0080830416 4.8801987e-08 3809.5201
3800 0.0080835355 5.0116105e-08 3809.7436
3810 0.0080840429 5.1537653e-08 3809.9733
3820 0.0080845652 5.3078583e-08 3810.2097
3830 0.0080851034 5.4752728e-08 3810.4535
3840 0.008085659 5.6576175e-08 3810.7054
3850 0.0080862335 5.8567743e-08 3810.9659
3860 0.0080868289 6.0749572e-08 3811.236
3870 0.008087447 6.3147889e-08 3811.5166
3880 0.0080880901 6.5793981e-08 3811.8087
3890 0.008088761 6.8725458e-08 3812.1136
3900 0.0080894626 7.1987928e-08 3812.4327
3910 0.0080901986 7.5637206e-08 3812.7675
3920 0.008090973 7.9742316e-08 3813.1201
3930 0.0080917909 8.4389592e-08 3813.4926
3940 0.008092658 8.9688414e-08 3813.8879
3950 0.0080935816 9.5779352e-08 3814.3091
3960 0.0080945703 1.0284601e-07 3814.7604
3970 0.0080956349 1.1113264e-07 3815.2467
3980 0.0080967891 1.2097115e-07 3815.7742
3990 0.0080980502 1.3282379e-07 3816.3511
4000 0.0080994413 1.4735308e-07 3816.9878
4010 0.0081009931 1.6554202e-07 3817.6987
4020 0.0081027486 1.8891116e-07 3818.5035
4030 0.0081047696 2.1993774e-07 3819.4308
4040 0.0081071501 2.6293325e-07 3820.524
4050 0.0081100418 3.2608623e-07 3821.8531
4060 0.0081137136 4.2695471e-07 3823.5422
4070 0.0081187073 6.1068659e-07 3825.8415
4080 0.0081263808 1.0353843e-06 3829.3781
4090 0.0081421033 2.8175459e-06 3836.6316
4100 0.0083319479 3.0660994e-05 3924.296
4110 0.0086521081 2.4031675e-05 4072.0381
4120 0.0089367803 5.8263834e-06 4203.2922
4130 0.0089679114 1.6262217e-06 4217.6293
4140 0.0089805825 9.6546502e-07 4223.4594
4150 0.0089889356 7.1159925e-07 4227.3001
4160 0.0089954101 5.8311893e-07 4230.2754
4170 0.0090008803 5.1000973e-07 4232.7881
4180 0.0090057682 4.6713078e-07 4235.0326
4190 0.0090103206 4.4370361e-07 4237.1225
4200 0.0090147071 4.3491502e-07 4239.1361
4210 0.0090190645 4.3912951e-07 4241.1362
4220 0.0090235243 4.570826e-07 4243.1834
4230 0.0090282367 4.9222468e-07 4245.3469
4240 0.0090334045 5.5254852e-07 4247.72
4250 0.0090393478 6.5600428e-07 4250.4502
4260 0.0090466656 8.4827393e-07 4253.8133
4270 0.0090567641 1.2818738e-06 4258.457
4280 0.0090746835 2.9033891e-06 4266.7027
4290 0.0092346752 2.9451638e-05 4340.3839
4300 0.0093466586 4.9023913e-06 4391.9319
4310 0.0093992941 7.8400922e-06 4416.149
4320 0.0097053159 4.3362296e-05 4556.9393
4330 0.010037349 4.9648086e-05 4709.5604
4340 0.010297354 8.8232096e-06 4828.9697
4350 0.010503113 4.4016316e-05 4923.4016
4360 0.010926633 4.2142313e-05 5117.622
4370 0.011318805 4.0285407e-05 5297.2575
4380 0.011746199 4.3755472e-05 5492.8047
4390 0.012044606 2.1150168e-05 5629.1924
4400 0.01231664 7.0784321e-06 5753.4243
4410 0.01236554 3.954763e-06 5775.7358
4420 0.012415 8.8450437e-06 5798.2999
4430 0.012723996 3.6113036e-05 5939.2622
4440 0.013109261 4.5827638e-05 6114.8493
4450 0.013251276 2.6649019e-06 6179.5172
4460 0.013269544 1.2200106e-06 6187.8251
4470 0.013279619 8.155501e-07 6192.4028
4480 0.013286853 6.3300974e-07 6195.6879
4490 0.01329269 5.3347649e-07 6198.3373
4500 0.013297735 4.7451627e-07 6200.6261
4510 0.013302306 4.392029e-07 6202.6992
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4570 0.013328439 5.1597347e-07 6214.5493
4580 0.01333395 6.0235495e-07 6217.0498
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4600 0.013349342 1.0699582e-06 6224.0388
4610 0.013363183 1.98365e-06 6230.3293
4620 0.013404081 1.4367775e-05 6248.9319
4630 0.013593325 3.787203e-06 6335.0239
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4680 0.013662041 1.0034733e-06 6366.2295
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4700 0.013686941 1.780995e-06 6377.5343
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4720 0.013968014 3.9765415e-05 6505.2802
4730 0.014228787 6.2632217e-06 6623.7185
4740 0.014278333 4.7934169e-06 6646.2018
4750 0.014382212 5.1069055e-05 6693.3424
4760 0.014525205 2.0381123e-06 6758.2178
4770 0.014538504 8.2250651e-07 6764.2412
4780 0.014544984 4.9114353e-07 6767.1723
4790 0.014549144 3.4212232e-07 6769.0518
4800 0.014552156 2.589287e-07 6770.4109
4810 0.014554491 2.0641662e-07 6771.4633
4820 0.014556384 1.7052382e-07 6772.315
4830 0.014557966 1.4457875e-07 6773.0262
4840 0.014559319 1.250293e-07 6773.6339
4850 0.014560498 1.09819e-07 6774.1626
4860 0.014561539 9.7678962e-08 6774.629
4870 0.01456247 8.7785899e-08 6775.0453
4880 0.01456331 7.9583482e-08 6775.4205
4890 0.014564074 7.2682934e-08 6775.7613
4900 0.014564773 6.6804784e-08 6776.0732
4910 0.014565418 6.1743238e-08 6776.3601
4920 0.014566015 5.7343571e-08 6776.6256
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4940 0.01456709 5.0082359e-08 6777.1026
4950 0.014567577 4.7055963e-08 6777.3183
4960 0.014568035 4.4350048e-08 6777.521
4970 0.014568467 4.1917669e-08 6777.712
4980 0.014568876 3.9720495e-08 6777.8926
4990 0.014569265 3.7726941e-08 6778.0636
5000 0.014569634 3.5910753e-08 6778.2261
Loop time of 24.155 on 1 procs for 5000 steps with 32000 atoms
Performance: 0.001 ns/day, 37368.951 hours/ns, 206.996 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 | 15.795 | 15.795 | 15.795 | 0.0 | 65.39
Neigh | 1.5182 | 1.5182 | 1.5182 | 0.0 | 6.29
Comm | 0.58555 | 0.58555 | 0.58555 | 0.0 | 2.42
Output | 0.0064323 | 0.0064323 | 0.0064323 | 0.0 | 0.03
Modify | 5.619 | 5.619 | 5.619 | 0.0 | 23.26
Other | | 0.6313 | | | 2.61
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13556 ave 13556 max 13556 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: 576016 ave 576016 max 576016 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 576016
Ave neighs/atom = 18.0005
Neighbor list builds = 68
Dangerous builds = 42
Total wall time: 0:00:24

597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4 Normal file
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@ -0,0 +1,597 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region rbox block -10 10 -10 10 -10 10
create_box 1 rbox
Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
1 by 2 by 2 MPI processor grid
mass 1 28.0855
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.000856161 secs
velocity all create 300 42534 mom yes rot yes
group gPKA id 1
1 atoms in group gPKA
velocity gPKA set 1120 1620 389
pair_style sw
pair_coeff * * Si.sw Si
Reading potential file Si.sw with DATE: 2007-06-11
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10
thermo_style custom step time dt f_fel
#compute ek all ke/atom
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.77118
ghost atom cutoff = 5.77118
binsize = 2.88559, bins = 38 38 38
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) fix electron/stopping, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.825 | 3.825 Mbytes
Step Time Dt f_fel
0 0 4.98128e-05 0
10 0.00030141235 7.4131221e-06 143.83474
20 0.00035951242 6.0314282e-06 171.53584
30 0.00057457861 3.511731e-05 274.07067
40 0.00086591115 5.8248574e-06 412.87352
50 0.00090045749 2.102773e-06 429.31482
60 0.00091828633 1.5369556e-06 437.79502
70 0.00093306208 1.4645168e-06 444.82135
80 0.00094861336 1.7491631e-06 452.21657
90 0.00097033523 3.0804023e-06 462.54893
100 0.0010792154 4.9075683e-05 514.37014
110 0.0012080866 2.3201427e-06 575.68827
120 0.0012239719 1.0507964e-06 583.23648
130 0.0012325518 6.8263389e-07 587.30975
140 0.0012385211 5.1201217e-07 590.14147
150 0.0012431661 4.1521773e-07 592.34347
160 0.001247021 3.5379338e-07 594.16984
170 0.0012503586 3.1202939e-07 595.75031
180 0.0012533374 2.8236002e-07 597.16021
190 0.0012560582 2.6071816e-07 598.44745
200 0.0012585895 2.4474279e-07 599.64465
210 0.001260981 2.3298831e-07 600.7754
220 0.0012632704 2.2454021e-07 601.85763
230 0.001265488 2.1881458e-07 602.90571
240 0.0012676591 2.154488e-07 603.93173
250 0.0012698064 2.1424147e-07 604.94641
260 0.0012719511 2.1512161e-07 605.9598
270 0.0012741141 2.1813836e-07 606.98189
280 0.0012763174 2.2346783e-07 608.02314
290 0.0012785856 2.3143942e-07 609.09518
300 0.0012809473 2.4258888e-07 610.2116
310 0.0012834376 2.5775518e-07 611.38916
320 0.0012861023 2.7825685e-07 612.64953
330 0.0012890034 3.062254e-07 614.02218
340 0.0012922301 3.4527805e-07 615.54956
350 0.0012959196 4.0200263e-07 617.29679
360 0.0013003 4.8966484e-07 619.37233
370 0.0013057965 6.3923294e-07 621.9783
380 0.00131335 9.423535e-07 625.56194
390 0.0013258073 1.8277087e-06 631.47661
400 0.0013653313 1.4985239e-05 650.25939
410 0.0016927117 4.5643592e-05 805.84388
420 0.002085671 2.5698185e-05 992.40957
430 0.0021935861 5.3102217e-06 1043.597
440 0.0022614637 1.5788858e-05 1075.7807
450 0.0025463923 1.6989456e-05 1210.8535
460 0.0029095455 3.9205279e-05 1382.8591
470 0.003309122 3.8882183e-05 1571.9128
480 0.0037129772 4.0573389e-05 1762.7749
490 0.004120209 2.7525742e-05 1955.0148
500 0.0042711049 1.9373612e-05 2026.1805
510 0.0045860203 2.4773305e-05 2174.6208
520 0.004995259 3.8017877e-05 2367.3335
530 0.0051457762 5.4205615e-06 2438.1475
540 0.005203221 8.8625579e-06 2465.1577
550 0.0054221421 5.7304442e-06 2568.0888
560 0.0054524345 1.5599386e-06 2582.3169
570 0.0054645073 9.1093243e-07 2587.9819
580 0.0054723338 6.6033575e-07 2591.6518
590 0.0054782965 5.3155858e-07 2594.446
600 0.005483241 4.5581839e-07 2596.7619
610 0.0054875675 4.0821885e-07 2598.7875
620 0.0054915013 3.7775507e-07 2600.6287
630 0.0054951861 3.5898561e-07 2602.3529
640 0.0054987249 3.4911444e-07 2604.0086
650 0.0055021998 3.4682698e-07 2605.6342
660 0.0055056844 3.5182676e-07 2607.2643
670 0.0055092538 3.6473743e-07 2608.9342
680 0.0055129936 3.8730595e-07 2610.6841
690 0.0055170145 4.2303997e-07 2612.566
700 0.0055214749 4.7876507e-07 2614.6542
710 0.0055266296 5.6863699e-07 2617.0684
720 0.0055329452 7.2626141e-07 2620.0278
730 0.0055414528 1.0527596e-06 2624.0166
740 0.0055553208 2.0371511e-06 2630.523
750 0.0056023478 2.2133456e-05 2652.6057
760 0.0059007346 3.8610962e-05 2792.7168
770 0.0062508505 3.9428337e-05 2956.9697
780 0.0063682296 2.1223153e-06 3011.9927
790 0.0063824196 9.0656948e-07 3018.6346
800 0.0063896741 5.6137676e-07 3022.0266
810 0.0063944906 4.0276465e-07 3024.2763
820 0.0063980771 3.1284015e-07 3025.9499
830 0.0064009279 2.5537602e-07 3027.2789
840 0.006403292 2.1569057e-07 3028.3801
850 0.0064053117 1.8674792e-07 3029.32
860 0.0064070756 1.6477015e-07 3030.1402
870 0.0064086425 1.4755386e-07 3030.8682
880 0.0064100535 1.3373048e-07 3031.5232
890 0.0064113381 1.2240666e-07 3032.1191
900 0.0064125183 1.1297538e-07 3032.6662
910 0.0064136112 1.0501022e-07 3033.1724
920 0.0064146298 9.8203162e-08 3033.6439
930 0.0064155847 9.2326368e-08 3034.0856
940 0.0064164843 8.7207794e-08 3034.5015
950 0.0064173357 8.2715188e-08 3034.8948
960 0.0064181446 7.8745279e-08 3035.2682
970 0.0064189159 7.5216291e-08 3035.6241
980 0.0064196535 7.2062662e-08 3035.9642
990 0.0064203612 6.9231241e-08 3036.2903
1000 0.0064210418 6.6678502e-08 3036.6038
1010 0.006421698 6.4368478e-08 3036.9059
1020 0.0064223321 6.2271202e-08 3037.1976
1030 0.0064229461 6.0361517e-08 3037.4799
1040 0.0064235417 5.8618162e-08 3037.7537
1050 0.0064241206 5.702305e-08 3038.0197
1060 0.0064246841 5.556071e-08 3038.2784
1070 0.0064252336 5.4217838e-08 3038.5306
1080 0.0064257701 5.2982939e-08 3038.7768
1090 0.0064262948 5.1846034e-08 3039.0174
1100 0.0064268085 5.079843e-08 3039.2529
1110 0.006427312 4.9832523e-08 3039.4837
1120 0.0064278063 4.8941643e-08 3039.7101
1130 0.0064282919 4.811992e-08 3039.9325
1140 0.0064287697 4.7362175e-08 3040.1512
1150 0.0064292401 4.6663831e-08 3040.3665
1160 0.0064297038 4.6020833e-08 3040.5786
1170 0.0064301613 4.5429586e-08 3040.7878
1180 0.0064306131 4.4886899e-08 3040.9944
1190 0.0064310597 4.4389937e-08 3041.1986
1200 0.0064315016 4.3936183e-08 3041.4005
1210 0.006431939 4.3523406e-08 3041.6003
1220 0.0064323725 4.3149628e-08 3041.7984
1230 0.0064328025 4.2813101e-08 3041.9947
1240 0.0064332292 4.2512286e-08 3042.1896
1250 0.0064336531 4.2245836e-08 3042.3831
1260 0.0064340745 4.201258e-08 3042.5755
1270 0.0064344937 4.1811507e-08 3042.7668
1280 0.006434911 4.1641759e-08 3042.9572
1290 0.0064353268 4.1502622e-08 3043.1469
1300 0.0064357413 4.1393513e-08 3043.336
1310 0.0064361549 4.1313982e-08 3043.5247
1320 0.0064365678 4.1263699e-08 3043.713
1330 0.0064369803 4.1242458e-08 3043.9012
1340 0.0064373927 4.125017e-08 3044.0893
1350 0.0064378054 4.1286866e-08 3044.2775
1360 0.0064382185 4.1352691e-08 3044.466
1370 0.0064386324 4.1447915e-08 3044.6548
1380 0.0064390475 4.1572925e-08 3044.8441
1390 0.0064394639 4.1728238e-08 3045.034
1400 0.0064398819 4.1914501e-08 3045.2247
1410 0.006440302 4.2132499e-08 3045.4163
1420 0.0064407245 4.2383163e-08 3045.6091
1430 0.0064411496 4.2667584e-08 3045.803
1440 0.0064415776 4.2987016e-08 3045.9983
1450 0.0064420091 4.33429e-08 3046.1952
1460 0.0064424443 4.3736874e-08 3046.3938
1470 0.0064428835 4.4170794e-08 3046.5944
1480 0.0064433274 4.4646761e-08 3046.797
1490 0.0064437761 4.5167139e-08 3047.0019
1500 0.0064442303 4.5734596e-08 3047.2093
1510 0.0064446904 4.6352132e-08 3047.4195
1520 0.0064451569 4.7023127e-08 3047.6327
1530 0.0064456303 4.7751389e-08 3047.849
1540 0.0064461114 4.8541214e-08 3048.0689
1550 0.0064466006 4.9397455e-08 3048.2926
1560 0.0064470987 5.0325606e-08 3048.5204
1570 0.0064476064 5.1331902e-08 3048.7527
1580 0.0064481245 5.2423434e-08 3048.9899
1590 0.006448654 5.3608296e-08 3049.2323
1600 0.0064491958 5.4895757e-08 3049.4804
1610 0.006449751 5.6296469e-08 3049.7347
1620 0.0064503207 5.7822727e-08 3049.9959
1630 0.0064509063 5.9488788e-08 3050.2644
1640 0.0064515092 6.1311263e-08 3050.5409
1650 0.0064521312 6.3309616e-08 3050.8263
1660 0.006452774 6.5506785e-08 3051.1214
1670 0.0064534398 6.7929981e-08 3051.4272
1680 0.0064541309 7.0611714e-08 3051.7448
1690 0.0064548502 7.3591127e-08 3052.0755
1700 0.0064556007 7.6915753e-08 3052.4207
1710 0.0064563863 8.064386e-08 3052.7823
1720 0.0064572113 8.4847627e-08 3053.1621
1730 0.0064580807 8.9617502e-08 3053.5627
1740 0.0064590008 9.5068304e-08 3053.9869
1750 0.006459979 1.0134793e-07 3054.4381
1760 0.0064610244 1.0865003e-07 3054.9206
1770 0.0064621483 1.1723301e-07 3055.4397
1780 0.0064633651 1.2744917e-07 3056.0021
1790 0.0064646931 1.3979108e-07 3056.6163
1800 0.0064661566 1.5496815e-07 3057.2937
1810 0.0064677883 1.7403894e-07 3058.0494
1820 0.006469634 1.9865267e-07 3058.9049
1830 0.0064717601 2.3152064e-07 3059.8912
1840 0.0064742682 2.7741818e-07 3061.0556
1850 0.0064773249 3.4556351e-07 3062.4759
1860 0.0064812294 4.5619653e-07 3064.2917
1870 0.0064866019 6.6337441e-07 3066.7924
1880 0.0064950748 1.1706786e-06 3070.7399
1890 0.0065140322 3.7878566e-06 3079.5809
1900 0.0066957122 6.7105464e-06 3164.3691
1910 0.0067279909 1.493224e-06 3179.4195
1920 0.0067392058 8.1410321e-07 3184.6428
1930 0.0067460435 5.5996376e-07 3187.8246
1940 0.0067509948 4.2936252e-07 3190.1267
1950 0.0067549055 3.5072462e-07 3191.9436
1960 0.0067581623 2.9865016e-07 3193.4556
1970 0.0067609737 2.6192794e-07 3194.7601
1980 0.0067634648 2.3486813e-07 3195.9153
1990 0.0067657165 2.1428715e-07 3196.9589
2000 0.0067677841 1.9827071e-07 3197.9167
2010 0.0067697074 1.8560268e-07 3198.8073
2020 0.006771516 1.7547663e-07 3199.6445
2030 0.0067732327 1.6733961e-07 3200.4388
2040 0.0067748755 1.6080268e-07 3201.1987
2050 0.0067764591 1.5558723e-07 3201.931
2060 0.0067779957 1.5149159e-07 3202.6414
2070 0.0067794958 1.4836976e-07 3203.3348
2080 0.0067809687 1.4611749e-07 3204.0155
2090 0.0067824227 1.4466322e-07 3204.6874
2100 0.0067838655 1.4396229e-07 3205.3542
2110 0.0067853047 1.4399348e-07 3206.0191
2120 0.0067867474 1.4475745e-07 3206.6858
2130 0.0067882012 1.4627671e-07 3207.3576
2140 0.0067896737 1.4859736e-07 3208.0381
2150 0.0067911733 1.5179256e-07 3208.7311
2160 0.0067927092 1.5596849e-07 3209.4411
2170 0.0067942917 1.6127347e-07 3210.1728
2180 0.0067959331 1.6791214e-07 3210.9319
2190 0.0067976479 1.7616698e-07 3211.7251
2200 0.0067994539 1.8643208e-07 3212.5608
2210 0.0068013736 1.9926751e-07 3213.4494
2220 0.0068034361 2.154897e-07 3214.4044
2230 0.0068056803 2.3632937e-07 3215.4441
2240 0.0068081604 2.6372257e-07 3216.5937
2250 0.0068109549 3.0088625e-07 3217.8897
2260 0.0068141846 3.5356212e-07 3219.3884
2270 0.0068180485 4.330391e-07 3221.1825
2280 0.0068229109 5.6479966e-07 3223.4417
2290 0.0068295488 8.2016289e-07 3226.5284
2300 0.0068401389 1.4950446e-06 3231.4568
2310 0.0068668194 6.4794351e-06 3243.8847
2320 0.0071339944 2.3817631e-05 3368.3827
2330 0.0074221156 3.4144405e-05 3502.5364
2340 0.007650075 3.3142879e-06 3608.5998
2350 0.0076703526 1.1927138e-06 3618.0215
2360 0.0076797526 7.185434e-07 3622.3847
2370 0.0076859146 5.1648342e-07 3625.2424
2380 0.0076905359 4.0623045e-07 3627.3839
2390 0.0076942651 3.3753265e-07 3629.1108
2400 0.0076974175 2.910504e-07 3630.5697
2410 0.0077001699 2.5780894e-07 3631.8426
2420 0.007702631 2.3309498e-07 3632.9803
2430 0.007704873 2.1420535e-07 3634.0161
2440 0.0077069459 1.9948463e-07 3634.9733
2450 0.0077088862 1.8786685e-07 3635.869
2460 0.0077107216 1.7863849e-07 3636.716
2470 0.0077124736 1.713078e-07 3637.5242
2480 0.0077141595 1.6552875e-07 3638.3017
2490 0.0077157937 1.6105508e-07 3639.0552
2500 0.0077173883 1.5771154e-07 3639.7903
2510 0.0077189541 1.553756e-07 3640.5121
2520 0.0077205008 1.539658e-07 3641.2249
2530 0.0077220373 1.534345e-07 3641.933
2540 0.0077235724 1.5376384e-07 3642.6405
2550 0.0077251148 1.5496427e-07 3643.3513
2560 0.0077266731 1.5707538e-07 3644.0695
2570 0.007728257 1.6016917e-07 3644.7995
2580 0.0077298765 1.6435633e-07 3645.5461
2590 0.0077315435 1.6979645e-07 3646.3147
2600 0.0077332712 1.7671412e-07 3647.1115
2610 0.0077350759 1.8542415e-07 3647.944
2620 0.0077369773 1.9637153e-07 3648.8214
2630 0.0077390006 2.1019669e-07 3649.7553
2640 0.0077411783 2.2784614e-07 3650.7609
2650 0.0077435548 2.5076917e-07 3651.8588
2660 0.0077461922 2.8128932e-07 3653.0779
2670 0.0077491826 3.233607e-07 3654.4608
2680 0.0077526703 3.8426634e-07 3656.0746
2690 0.0077569014 4.7896536e-07 3658.0337
2700 0.0077623476 6.435095e-07 3660.5572
2710 0.0077700972 9.9066415e-07 3664.1508
2720 0.0077837321 2.1192489e-06 3670.4787
2730 0.0078537309 5.0478452e-05 3702.9978
2740 0.0080019842 2.234588e-06 3771.8639
2750 0.0080167983 9.3912008e-07 3778.7349
2760 0.0080243022 5.7998894e-07 3782.2116
2770 0.0080292782 4.1619434e-07 3784.5147
2780 0.0080329859 3.2365852e-07 3786.2291
2790 0.0080359374 2.6464667e-07 3787.5927
2800 0.0080383893 2.2394834e-07 3788.7244
2810 0.0080404882 1.9429813e-07 3789.6924
2820 0.0080423251 1.7180333e-07 3790.5389
2830 0.0080439606 1.5419708e-07 3791.292
2840 0.0080454366 1.4007294e-07 3791.9711
2850 0.0080467835 1.2851365e-07 3792.5904
2860 0.0080480239 1.1889632e-07 3793.1603
2870 0.0080491753 1.1078364e-07 3793.689
2880 0.0080502511 1.0385986e-07 3794.1826
2890 0.0080512621 9.7891518e-08 3794.6462
2900 0.0080522171 9.2702379e-08 3795.0838
2910 0.0080531232 8.815703e-08 3795.4988
2920 0.0080539863 8.4149767e-08 3795.8939
2930 0.0080548115 8.0596927e-08 3796.2714
2940 0.0080556029 7.7431468e-08 3796.6332
2950 0.0080563642 7.4599072e-08 3796.9811
2960 0.0080570985 7.2055292e-08 3797.3166
2970 0.0080578086 6.9763432e-08 3797.6407
2980 0.0080584967 6.7692955e-08 3797.9548
2990 0.0080591651 6.5818259e-08 3798.2596
3000 0.0080598155 6.4117744e-08 3798.5562
3010 0.0080604496 6.2573076e-08 3798.8452
3020 0.0080610689 6.1168613e-08 3799.1273
3030 0.0080616747 5.9890948e-08 3799.4033
3040 0.0080622683 5.8728542e-08 3799.6735
3050 0.0080628507 5.7671429e-08 3799.9386
3060 0.0080634231 5.6710976e-08 3800.199
3070 0.0080639862 5.5839691e-08 3800.4551
3080 0.008064541 5.5051058e-08 3800.7074
3090 0.0080650882 5.4339406e-08 3800.9562
3100 0.0080656287 5.3699803e-08 3801.2018
3110 0.008066163 5.3127961e-08 3801.4446
3120 0.008066692 5.2620159e-08 3801.6849
3130 0.0080672161 5.2173187e-08 3801.923
3140 0.0080677361 5.1784286e-08 3802.1591
3150 0.0080682524 5.1451107e-08 3802.3936
3160 0.0080687656 5.1171678e-08 3802.6266
3170 0.0080692762 5.0944369e-08 3802.8584
3180 0.0080697848 5.0767875e-08 3803.0892
3190 0.0080702919 5.064119e-08 3803.3194
3200 0.0080707979 5.0563598e-08 3803.549
3210 0.0080713034 5.0534662e-08 3803.7784
3220 0.0080718088 5.0554215e-08 3804.0077
3230 0.0080723146 5.0622362e-08 3804.2373
3240 0.0080728213 5.073948e-08 3804.4672
3250 0.0080733294 5.090622e-08 3804.6978
3260 0.0080738394 5.1123521e-08 3804.9292
3270 0.0080743518 5.139262e-08 3805.1618
3280 0.0080748671 5.171507e-08 3805.3957
3290 0.0080753859 5.2092761e-08 3805.6311
3300 0.0080759088 5.2527952e-08 3805.8685
3310 0.0080764362 5.3023303e-08 3806.1079
3320 0.0080769689 5.3581914e-08 3806.3498
3330 0.0080775075 5.4207378e-08 3806.5944
3340 0.0080780526 5.4903844e-08 3806.842
3350 0.0080786051 5.567608e-08 3807.093
3360 0.0080791656 5.652957e-08 3807.3477
3370 0.0080797351 5.7470611e-08 3807.6065
3380 0.0080803144 5.8506444e-08 3807.8698
3390 0.0080809045 5.9645402e-08 3808.1381
3400 0.0080815065 6.0897097e-08 3808.412
3410 0.0080821215 6.2272649e-08 3808.6918
3420 0.0080827509 6.3784959e-08 3808.9782
3430 0.0080833961 6.5449061e-08 3809.272
3440 0.0080840587 6.7282544e-08 3809.5737
3450 0.0080847405 6.9306098e-08 3809.8843
3460 0.0080854434 7.1544197e-08 3810.2047
3470 0.0080861698 7.402597e-08 3810.5359
3480 0.0080869223 7.6786336e-08 3810.8791
3490 0.0080877037 7.9867475e-08 3811.2357
3500 0.0080885176 8.3320783e-08 3811.6073
3510 0.0080893679 8.7209484e-08 3811.9957
3520 0.0080902594 9.1612182e-08 3812.4031
3530 0.0080911975 9.662777e-08 3812.8321
3540 0.008092189 1.0238234e-07 3813.2857
3550 0.008093242 1.0903907e-07 3813.7677
3560 0.0080943663 1.1681285e-07 3814.2827
3570 0.0080955744 1.2599212e-07 3814.8364
3580 0.0080968821 1.3697303e-07 3815.4361
3590 0.0080983096 1.5031413e-07 3816.0912
3600 0.008099884 1.6682798e-07 3816.8142
3610 0.0081016421 1.877419e-07 3817.6222
3620 0.0081036359 2.1499717e-07 3818.5391
3630 0.0081059419 2.5184713e-07 3819.6004
3640 0.0081086795 3.041685e-07 3820.8614
3650 0.0081120491 3.8370792e-07 3822.4147
3660 0.0081164246 5.1761443e-07 3824.4335
3670 0.0081226282 7.8476649e-07 3827.2984
3680 0.0081330874 1.5377267e-06 3832.133
3690 0.0081640997 9.4754571e-06 3846.4828
3700 0.0084647088 3.6520628e-05 3985.6105
3710 0.0087788105 5.0607918e-05 4130.8576
3720 0.0089496823 2.7369422e-06 4209.8144
3730 0.0089676915 1.1442905e-06 4218.1247
3740 0.0089769276 7.2591487e-07 4222.3827
3750 0.0089832427 5.3867242e-07 4225.2918
3760 0.0089881163 4.3436406e-07 4227.5353
3770 0.0089921427 3.689283e-07 4229.3876
3780 0.0089956201 3.2480899e-07 4230.9866
3790 0.0089987196 2.9368682e-07 4232.4111
3800 0.0090015492 2.7114137e-07 4233.711
3810 0.0090041821 2.5463023e-07 4234.9202
3820 0.0090066711 2.4261002e-07 4236.0629
3830 0.0090090563 2.3411372e-07 4237.1578
3840 0.0090113701 2.2853263e-07 4238.2196
3850 0.0090136398 2.2549889e-07 4239.2611
3860 0.0090158898 2.2482231e-07 4240.2936
3870 0.0090181435 2.264602e-07 4241.3277
3880 0.0090204243 2.3051066e-07 4242.3742
3890 0.0090227572 2.3722751e-07 4243.4449
3900 0.0090251709 2.4706119e-07 4244.5528
3910 0.0090276995 2.6073849e-07 4245.7136
3920 0.0090303862 2.7940938e-07 4246.9474
3930 0.0090332884 3.0492215e-07 4248.2805
3940 0.0090364872 3.4036714e-07 4249.7505
3950 0.0090401038 3.9124064e-07 4251.4133
3960 0.0090443343 4.6822852e-07 4253.3593
3970 0.0090495296 5.9498137e-07 4255.7504
3980 0.0090564177 8.3552398e-07 4258.9229
3990 0.0090669429 1.4384739e-06 4263.774
4000 0.0090904831 4.9111984e-06 4274.6331
4010 0.0092929124 8.3135371e-06 4368.0633
4020 0.0093414419 3.1334206e-06 4390.4447
4030 0.0093714047 3.1966251e-06 4404.2581
4040 0.0094176451 9.8265197e-06 4425.5788
4050 0.0097772862 4.2787238e-05 4591.3956
4060 0.010043914 5.0703357e-05 4714.2148
4070 0.010275503 5.9586189e-06 4820.8179
4080 0.010329372 6.4730027e-06 4845.5948
4090 0.010580719 3.2675549e-05 4961.1991
4100 0.01097933 4.1824022e-05 5144.3777
4110 0.011375225 4.4528389e-05 5326.1041
4120 0.011791986 4.4629128e-05 5517.1914
4130 0.012199057 3.8467532e-05 5703.6209
4140 0.012388718 1.6598211e-05 5790.3997
4150 0.012719145 2.6617697e-05 5941.4863
4160 0.013138874 3.9714695e-05 6133.2127
4170 0.013296898 5.7028372e-06 6205.3279
4180 0.013359491 1.0623338e-05 6233.8756
4190 0.013580279 4.9259166e-06 6334.5676
4200 0.013608204 1.5476759e-06 6347.2885
4210 0.013620408 9.4152281e-07 6352.8431
4220 0.013628594 7.0110358e-07 6356.5664
4230 0.01363499 5.7777895e-07 6359.474
4240 0.013640419 5.071712e-07 6361.941
4250 0.013645286 4.6571283e-07 6364.1515
4260 0.013649829 4.4320314e-07 6366.2145
4270 0.013654213 4.3508698e-07 6368.2055
4280 0.013658575 4.3986766e-07 6370.186
4290 0.013663045 4.5837677e-07 6372.2157
4300 0.013667773 4.9416073e-07 6374.363
4310 0.013672963 5.5535604e-07 6376.7211
4320 0.01367894 6.6021298e-07 6379.4372
4330 0.013686311 8.5526524e-07 6382.7882
4340 0.013696507 1.296644e-06 6387.4262
4350 0.013714701 2.9652221e-06 6395.7088
4360 0.013881439 3.5899661e-05 6471.6738
4370 0.014196617 3.1253608e-05 6615.1811
4380 0.014504048 7.0683429e-06 6755.0394
4390 0.014536871 1.4515319e-06 6769.9538
4400 0.014547629 7.6742092e-07 6774.8365
4410 0.01455401 5.1561918e-07 6777.7294
4420 0.014558528 3.8717171e-07 6779.7758
4430 0.014562024 3.1004583e-07 6781.3579
4440 0.014564879 2.5893679e-07 6782.6486
4450 0.014567296 2.2275131e-07 6783.7406
4460 0.014569397 1.9588676e-07 6784.6888
4470 0.014571258 1.7521879e-07 6785.5285
4480 0.014572934 1.5887218e-07 6786.2838
4490 0.014574461 1.4565562e-07 6786.9717
4500 0.014575867 1.3477717e-07 6787.6046
4510 0.014577173 1.2569059e-07 6788.1919
4520 0.014578394 1.1800737e-07 6788.741
4530 0.014579544 1.1144387e-07 6789.2576
4540 0.014580632 1.0578845e-07 6789.7464
4550 0.014581667 1.0088007e-07 6790.2111
4560 0.014582656 9.6594222e-08 6790.6548
4570 0.014583605 9.283317e-08 6791.0802
4580 0.014584518 8.9519251e-08 6791.4895
4590 0.0145854 8.6590045e-08 6791.8845
4600 0.014586254 8.3994895e-08 6792.267
4610 0.014587083 8.1692339e-08 6792.6383
4620 0.014587891 7.9648193e-08 6792.9997
4630 0.014588679 7.7834097e-08 6793.3523
4640 0.01458945 7.6226411e-08 6793.6971
4650 0.014590205 7.4805352e-08 6794.035
4660 0.014590948 7.3554327e-08 6794.3668
4670 0.014591678 7.2459408e-08 6794.6932
4680 0.014592398 7.1508917e-08 6795.015
4690 0.01459311 7.0693097e-08 6795.3328
4700 0.014593813 7.0003852e-08 6795.6471
4710 0.014594511 6.9434537e-08 6795.9585
4720 0.014595203 6.8979799e-08 6796.2676
4730 0.014595891 6.8635445e-08 6796.5748
4740 0.014596576 6.839835e-08 6796.8807
4750 0.01459726 6.8266383e-08 6797.1857
4760 0.014597942 6.823836e-08 6797.4903
4770 0.014598625 6.8314021e-08 6797.795
4780 0.014599309 6.849402e-08 6798.1003
4790 0.014599995 6.8779943e-08 6798.4065
4800 0.014600684 6.9174339e-08 6798.7143
4810 0.014601378 6.9680779e-08 6799.0241
4820 0.014602078 7.0303936e-08 6799.3364
4830 0.014602784 7.1049693e-08 6799.6517
4840 0.014603498 7.1925284e-08 6799.9707
4850 0.014604222 7.2939475e-08 6800.294
4860 0.014604956 7.4102791e-08 6800.6221
4870 0.014605703 7.5427802e-08 6800.9557
4880 0.014606464 7.6929481e-08 6801.2958
4890 0.014607241 7.8625665e-08 6801.643
4900 0.014608036 8.0537626e-08 6801.9983
4910 0.01460885 8.2690811e-08 6802.3627
4920 0.014609688 8.5115787e-08 6802.7374
4930 0.014610551 8.7849474e-08 6803.1237
4940 0.014611443 9.0936752e-08 6803.5231
4950 0.014612368 9.4432608e-08 6803.9372
4960 0.01461333 9.8405013e-08 6804.3681
4970 0.014614334 1.0293885e-07 6804.8181
4980 0.014615386 1.0814135e-07 6805.2899
4990 0.014616494 1.1414984e-07 6805.7869
5000 0.014617666 1.2114278e-07 6806.313
Loop time of 9.26846 on 4 procs for 5000 steps with 32000 atoms
Performance: 0.006 ns/day, 4250.474 hours/ns, 539.464 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6281 | 4.7789 | 5.1937 | 11.0 | 51.56
Neigh | 0.40488 | 0.41576 | 0.43895 | 2.1 | 4.49
Comm | 0.8478 | 1.2799 | 1.4349 | 22.1 | 13.81
Output | 0.0048099 | 0.016429 | 0.050251 | 15.2 | 0.18
Modify | 2.1042 | 2.1347 | 2.1706 | 1.6 | 23.03
Other | | 0.6427 | | | 6.93
Nlocal: 8000 ave 8033 max 7977 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 6061.25 ave 6085 max 6028 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 144002 ave 144601 max 143596 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 576008
Ave neighs/atom = 18.0003
Neighbor list builds = 67
Dangerous builds = 38
Total wall time: 0:00:09

196
examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.1 Normal file
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LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 1
Lattice spacing in x,y,z = 1 1 1
region rbox block -100 100 -100 100 -100 100
region rsmallbox block -90 90 -90 90 -90 90
create_box 1 rbox
Created orthogonal box = (-100 -100 -100) to (100 100 100)
1 by 1 by 1 MPI processor grid
mass 1 28.0855
create_atoms 1 single 0 0 0
Created 1 atoms
create_atoms CPU = 4.05312e-06 secs
velocity all set 1120 1620 389
pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom
compute ektot all reduce sum c_ek
thermo 100
thermo_style custom step time dt f_fel c_ektot
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 134 134 134
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix electron/stopping, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.31 | 13.31 | 13.31 Mbytes
Step Time Dt f_fel c_ektot
0 0 4.98128e-05 0 5865.5525
100 0.0049972222 5.0137252e-05 76.048699 5789.883
200 0.010027278 5.0467945e-05 151.67477 5714.2548
300 0.015090636 5.0803375e-05 226.8806 5639.0469
400 0.020187777 5.1143663e-05 301.6685 5564.2569
500 0.025319192 5.1488933e-05 376.04082 5489.8825
600 0.030485386 5.1839314e-05 449.99984 5415.9215
700 0.035686876 5.2194938e-05 523.54788 5342.3714
800 0.040924195 5.2555944e-05 596.68721 5269.23
900 0.046197886 5.2922477e-05 669.42011 5196.4951
1000 0.05150851 5.3294685e-05 741.74883 5124.1643
1100 0.056856642 5.3672723e-05 813.67563 5052.2355
1200 0.062229338 5.3731851e-05 824.43012 5041.1224
1300 0.067602524 5.3731851e-05 824.43012 5041.1224
1400 0.072978188 5.387166e-05 850.91948 5014.9907
1500 0.07838447 5.425887e-05 922.23961 4943.6685
1600 0.08382978 5.4652329e-05 993.16341 4872.7428
1700 0.089299984 5.4705935e-05 1002.3545 4863.198
1800 0.094770578 5.4705935e-05 1002.3545 4863.198
1900 0.10024117 5.4705935e-05 1002.3545 4863.198
2000 0.10571333 5.4819488e-05 1022.8338 4843.0716
2100 0.11121515 5.5222127e-05 1093.1986 4772.7048
2200 0.11675757 5.5631458e-05 1163.1724 4702.7291
2300 0.12234126 5.6047675e-05 1232.7573 4633.1422
2400 0.12796692 5.6470985e-05 1301.9555 4563.942
2500 0.13363527 5.6901598e-05 1370.7692 4495.1264
2600 0.13934706 5.7339739e-05 1439.2006 4426.6932
2700 0.14510304 5.7785637e-05 1507.2516 4358.6403
2800 0.150904 5.8239536e-05 1574.9245 4290.9655
2900 0.15675076 5.8701688e-05 1642.2213 4223.6668
3000 0.16264416 5.9172358e-05 1709.1441 4156.7422
3100 0.16858505 5.9651822e-05 1775.695 4090.1894
3200 0.17457434 6.0140369e-05 1841.8761 4024.0064
3300 0.18061294 6.0638302e-05 1907.6894 3958.1913
3400 0.18669814 6.0949329e-05 1947.6558 3917.8967
3500 0.19279307 6.0949329e-05 1947.6558 3917.8967
3600 0.198888 6.0949329e-05 1947.6558 3917.8967
3700 0.20498294 6.0949329e-05 1947.6558 3917.8967
3800 0.21107787 6.0949329e-05 1947.6558 3917.8967
3900 0.2171728 6.0949329e-05 1947.6558 3917.8967
4000 0.22326773 6.0949329e-05 1947.6558 3917.8967
4100 0.22936267 6.0949329e-05 1947.6558 3917.8967
4200 0.2354576 6.0949329e-05 1947.6558 3917.8967
4300 0.24155253 6.0949329e-05 1947.6558 3917.8967
4400 0.24764747 6.0949329e-05 1947.6558 3917.8967
4500 0.2537424 6.0949329e-05 1947.6558 3917.8967
4600 0.25983733 6.0949329e-05 1947.6558 3917.8967
4700 0.26593227 6.0949329e-05 1947.6558 3917.8967
4800 0.2720272 6.0949329e-05 1947.6558 3917.8967
4900 0.27812213 6.0949329e-05 1947.6558 3917.8967
5000 0.28421706 6.0949329e-05 1947.6558 3917.8967
5100 0.290312 6.0949329e-05 1947.6558 3917.8967
5200 0.29640693 6.0949329e-05 1947.6558 3917.8967
5300 0.30250186 6.0949329e-05 1947.6558 3917.8967
5400 0.3085968 6.0949329e-05 1947.6558 3917.8967
5500 0.31469173 6.0949329e-05 1947.6558 3917.8967
5600 0.32078666 6.0949329e-05 1947.6558 3917.8967
5700 0.32688159 6.0949329e-05 1947.6558 3917.8967
5800 0.33297653 6.0949329e-05 1947.6558 3917.8967
5900 0.33907146 6.0949329e-05 1947.6558 3917.8967
6000 0.34516639 6.0949329e-05 1947.6558 3917.8967
6100 0.35126133 6.0949329e-05 1947.6558 3917.8967
6200 0.35735626 6.0949329e-05 1947.6558 3917.8967
6300 0.36345119 6.0949329e-05 1947.6558 3917.8967
6400 0.36954612 6.0949329e-05 1947.6558 3917.8967
6500 0.37564106 6.0949329e-05 1947.6558 3917.8967
6600 0.38173599 6.0949329e-05 1947.6558 3917.8967
6700 0.38783092 6.0949329e-05 1947.6558 3917.8967
6800 0.39392586 6.0949329e-05 1947.6558 3917.8967
6900 0.40002079 6.0949329e-05 1947.6558 3917.8967
7000 0.40611572 6.0949329e-05 1947.6558 3917.8967
7100 0.41221066 6.0949329e-05 1947.6558 3917.8967
7200 0.41830559 6.0949329e-05 1947.6558 3917.8967
7300 0.42440052 6.0949329e-05 1947.6558 3917.8967
7400 0.43049545 6.0949329e-05 1947.6558 3917.8967
7500 0.43659039 6.0949329e-05 1947.6558 3917.8967
7600 0.44268532 6.0949329e-05 1947.6558 3917.8967
7700 0.44878025 6.0949329e-05 1947.6558 3917.8967
7800 0.45487519 6.0949329e-05 1947.6558 3917.8967
7900 0.46097012 6.0949329e-05 1947.6558 3917.8967
8000 0.46706505 6.0949329e-05 1947.6558 3917.8967
8100 0.47315998 6.0949329e-05 1947.6558 3917.8967
8200 0.47925492 6.0949329e-05 1947.6558 3917.8967
8300 0.48534985 6.0949329e-05 1947.6558 3917.8967
8400 0.49144478 6.0949329e-05 1947.6558 3917.8967
8500 0.49753972 6.0949329e-05 1947.6558 3917.8967
8600 0.50363465 6.0949329e-05 1947.6558 3917.8967
8700 0.50972958 6.0949329e-05 1947.6558 3917.8967
8800 0.51582452 6.0949329e-05 1947.6558 3917.8967
8900 0.52191945 6.0949329e-05 1947.6558 3917.8967
9000 0.52801438 6.0949329e-05 1947.6558 3917.8967
9100 0.53410931 6.0949329e-05 1947.6558 3917.8967
9200 0.54020425 6.0949329e-05 1947.6558 3917.8967
9300 0.54629918 6.0949329e-05 1947.6558 3917.8967
9400 0.55239411 6.0949329e-05 1947.6558 3917.8967
9500 0.55848905 6.0949329e-05 1947.6558 3917.8967
9600 0.56458398 6.0949329e-05 1947.6558 3917.8967
9700 0.57067891 6.0949329e-05 1947.6558 3917.8967
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
Loop time of 1.25184 on 1 procs for 10000 steps with 1 atoms
Performance: 42.066 ns/day, 0.571 hours/ns, 7988.216 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0005827 | 0.0005827 | 0.0005827 | 0.0 | 0.05
Neigh | 1.2134 | 1.2134 | 1.2134 | 0.0 | 96.93
Comm | 0.02822 | 0.02822 | 0.02822 | 0.0 | 2.25
Output | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 0.14
Modify | 0.0052147 | 0.0052147 | 0.0052147 | 0.0 | 0.42
Other | | 0.002664 | | | 0.21
Nlocal: 1 ave 1 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 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: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 960
Dangerous builds = 568
Total wall time: 0:00:01

196
examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.4 Normal file
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@ -0,0 +1,196 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
units metal
boundary p p p
timestep 0.0001
lattice fcc 1
Lattice spacing in x,y,z = 1 1 1
region rbox block -100 100 -100 100 -100 100
region rsmallbox block -90 90 -90 90 -90 90
create_box 1 rbox
Created orthogonal box = (-100 -100 -100) to (100 100 100)
1 by 2 by 2 MPI processor grid
mass 1 28.0855
create_atoms 1 single 0 0 0
Created 1 atoms
create_atoms CPU = 1.19209e-05 secs
velocity all set 1120 1620 389
pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom
compute ektot all reduce sum c_ek
thermo 100
thermo_style custom step time dt f_fel c_ektot
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 134 134 134
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix electron/stopping, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.637 | 4.2 | 5.887 Mbytes
Step Time Dt f_fel c_ektot
0 0 4.98128e-05 0 5865.5525
100 0.0049972222 5.0137252e-05 76.048699 5789.883
200 0.010027278 5.0467945e-05 151.67477 5714.2548
300 0.015090636 5.0803375e-05 226.8806 5639.0469
400 0.020187777 5.1143663e-05 301.6685 5564.2569
500 0.025319192 5.1488933e-05 376.04082 5489.8825
600 0.030485386 5.1839314e-05 449.99984 5415.9215
700 0.035686876 5.2194938e-05 523.54788 5342.3714
800 0.040924195 5.2555944e-05 596.68721 5269.23
900 0.046197886 5.2922477e-05 669.42011 5196.4951
1000 0.05150851 5.3294685e-05 741.74883 5124.1643
1100 0.056856642 5.3672723e-05 813.67563 5052.2355
1200 0.062229338 5.3731851e-05 824.43012 5041.1224
1300 0.067602524 5.3731851e-05 824.43012 5041.1224
1400 0.072978188 5.387166e-05 850.91948 5014.9907
1500 0.07838447 5.425887e-05 922.23961 4943.6685
1600 0.08382978 5.4652329e-05 993.16341 4872.7428
1700 0.089299984 5.4705935e-05 1002.3545 4863.198
1800 0.094770578 5.4705935e-05 1002.3545 4863.198
1900 0.10024117 5.4705935e-05 1002.3545 4863.198
2000 0.10571333 5.4819488e-05 1022.8338 4843.0716
2100 0.11121515 5.5222127e-05 1093.1986 4772.7048
2200 0.11675757 5.5631458e-05 1163.1724 4702.7291
2300 0.12234126 5.6047675e-05 1232.7573 4633.1422
2400 0.12796692 5.6470985e-05 1301.9555 4563.942
2500 0.13363527 5.6901598e-05 1370.7692 4495.1264
2600 0.13934706 5.7339739e-05 1439.2006 4426.6932
2700 0.14510304 5.7785637e-05 1507.2516 4358.6403
2800 0.150904 5.8239536e-05 1574.9245 4290.9655
2900 0.15675076 5.8701688e-05 1642.2213 4223.6668
3000 0.16264416 5.9172358e-05 1709.1441 4156.7422
3100 0.16858505 5.9651822e-05 1775.695 4090.1894
3200 0.17457434 6.0140369e-05 1841.8761 4024.0064
3300 0.18061294 6.0638302e-05 1907.6894 3958.1913
3400 0.18669814 6.0949329e-05 1947.6558 3917.8967
3500 0.19279307 6.0949329e-05 1947.6558 3917.8967
3600 0.198888 6.0949329e-05 1947.6558 3917.8967
3700 0.20498294 6.0949329e-05 1947.6558 3917.8967
3800 0.21107787 6.0949329e-05 1947.6558 3917.8967
3900 0.2171728 6.0949329e-05 1947.6558 3917.8967
4000 0.22326773 6.0949329e-05 1947.6558 3917.8967
4100 0.22936267 6.0949329e-05 1947.6558 3917.8967
4200 0.2354576 6.0949329e-05 1947.6558 3917.8967
4300 0.24155253 6.0949329e-05 1947.6558 3917.8967
4400 0.24764747 6.0949329e-05 1947.6558 3917.8967
4500 0.2537424 6.0949329e-05 1947.6558 3917.8967
4600 0.25983733 6.0949329e-05 1947.6558 3917.8967
4700 0.26593227 6.0949329e-05 1947.6558 3917.8967
4800 0.2720272 6.0949329e-05 1947.6558 3917.8967
4900 0.27812213 6.0949329e-05 1947.6558 3917.8967
5000 0.28421706 6.0949329e-05 1947.6558 3917.8967
5100 0.290312 6.0949329e-05 1947.6558 3917.8967
5200 0.29640693 6.0949329e-05 1947.6558 3917.8967
5300 0.30250186 6.0949329e-05 1947.6558 3917.8967
5400 0.3085968 6.0949329e-05 1947.6558 3917.8967
5500 0.31469173 6.0949329e-05 1947.6558 3917.8967
5600 0.32078666 6.0949329e-05 1947.6558 3917.8967
5700 0.32688159 6.0949329e-05 1947.6558 3917.8967
5800 0.33297653 6.0949329e-05 1947.6558 3917.8967
5900 0.33907146 6.0949329e-05 1947.6558 3917.8967
6000 0.34516639 6.0949329e-05 1947.6558 3917.8967
6100 0.35126133 6.0949329e-05 1947.6558 3917.8967
6200 0.35735626 6.0949329e-05 1947.6558 3917.8967
6300 0.36345119 6.0949329e-05 1947.6558 3917.8967
6400 0.36954612 6.0949329e-05 1947.6558 3917.8967
6500 0.37564106 6.0949329e-05 1947.6558 3917.8967
6600 0.38173599 6.0949329e-05 1947.6558 3917.8967
6700 0.38783092 6.0949329e-05 1947.6558 3917.8967
6800 0.39392586 6.0949329e-05 1947.6558 3917.8967
6900 0.40002079 6.0949329e-05 1947.6558 3917.8967
7000 0.40611572 6.0949329e-05 1947.6558 3917.8967
7100 0.41221066 6.0949329e-05 1947.6558 3917.8967
7200 0.41830559 6.0949329e-05 1947.6558 3917.8967
7300 0.42440052 6.0949329e-05 1947.6558 3917.8967
7400 0.43049545 6.0949329e-05 1947.6558 3917.8967
7500 0.43659039 6.0949329e-05 1947.6558 3917.8967
7600 0.44268532 6.0949329e-05 1947.6558 3917.8967
7700 0.44878025 6.0949329e-05 1947.6558 3917.8967
7800 0.45487519 6.0949329e-05 1947.6558 3917.8967
7900 0.46097012 6.0949329e-05 1947.6558 3917.8967
8000 0.46706505 6.0949329e-05 1947.6558 3917.8967
8100 0.47315998 6.0949329e-05 1947.6558 3917.8967
8200 0.47925492 6.0949329e-05 1947.6558 3917.8967
8300 0.48534985 6.0949329e-05 1947.6558 3917.8967
8400 0.49144478 6.0949329e-05 1947.6558 3917.8967
8500 0.49753972 6.0949329e-05 1947.6558 3917.8967
8600 0.50363465 6.0949329e-05 1947.6558 3917.8967
8700 0.50972958 6.0949329e-05 1947.6558 3917.8967
8800 0.51582452 6.0949329e-05 1947.6558 3917.8967
8900 0.52191945 6.0949329e-05 1947.6558 3917.8967
9000 0.52801438 6.0949329e-05 1947.6558 3917.8967
9100 0.53410931 6.0949329e-05 1947.6558 3917.8967
9200 0.54020425 6.0949329e-05 1947.6558 3917.8967
9300 0.54629918 6.0949329e-05 1947.6558 3917.8967
9400 0.55239411 6.0949329e-05 1947.6558 3917.8967
9500 0.55848905 6.0949329e-05 1947.6558 3917.8967
9600 0.56458398 6.0949329e-05 1947.6558 3917.8967
9700 0.57067891 6.0949329e-05 1947.6558 3917.8967
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
Loop time of 1.38891 on 4 procs for 10000 steps with 1 atoms
Performance: 37.915 ns/day, 0.633 hours/ns, 7199.876 timesteps/s
94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0004971 | 0.00060463 | 0.00069618 | 0.0 | 0.04
Neigh | 1.1005 | 1.1507 | 1.2839 | 7.2 | 82.85
Comm | 0.025918 | 0.026382 | 0.027041 | 0.3 | 1.90
Output | 0.0016336 | 0.005001 | 0.01507 | 8.2 | 0.36
Modify | 0.059378 | 0.20196 | 0.25453 | 18.3 | 14.54
Other | | 0.00422 | | | 0.30
Nlocal: 0.25 ave 1 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 960
Dangerous builds = 568
Total wall time: 0:00:01

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examples/hyper/in.hyper.global
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@ -12,6 +12,8 @@ variable cutevent index 1.1
variable steps index 100000
variable nevent index 1000
variable zoom index 1.8
variable seed index 826626413
variable tol index 1.0e-15
units metal
atom_style atomic
@ -45,7 +47,7 @@ neighbor 0.5 bin
neigh_modify every 1 delay 5 check yes
fix 1 mobile nve
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 858872873 zero yes
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
timestep 0.005
@ -92,4 +94,4 @@ dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
# run
hyper ${steps} ${nevent} HG event min 1.0e-6 1.0e-6 100 100 dump 1
hyper ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1

6
examples/hyper/in.hyper.local
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@ -107,6 +107,12 @@ dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
# test of histogramming and dump output of bias coeffs
#fix histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL &
# mode vector kind local file tmp.histo
#dump 2 all local 1000 tmp.local f_HL
# run
hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1

0
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@ -1,993 +0,0 @@
LAMMPS (10 Oct 2018)
# 3d EAM surface for local HD
# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
# hop event on (100) surface is same distance
# exchange event is 2 atoms moving same distance
variable Tequil index 400.0
variable Vmax index 0.4
variable qfactor index 0.3
variable cutbond index 3.2
variable Dcut index 10.0
variable cutevent index 1.1
variable alpha index 200.0
variable boost index 4000.0
variable ghostcut index 12.0
variable steps index 1500
variable nevent index 100
variable nx index 8
variable ny index 8
variable zoom index 1.8
variable seed index 826626413
variable tol index 1.0e-15
variable add index 37K
units metal
atom_style atomic
atom_modify map array
boundary p p p
comm_modify cutoff ${ghostcut}
comm_modify cutoff 12.0
lattice fcc 3.92
Lattice spacing in x,y,z = 3.92 3.92 3.92
region box block 0 6 0 6 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (23.52 23.52 15.68)
2 by 4 by 2 MPI processor grid
create_atoms 1 box
Created 576 atoms
Time spent = 0.00108504 secs
mass * 1.0
change_box all z final -0.1 5.0 boundary p p f
orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6)
# replicate in xy
replicate ${nx} ${ny} 1
replicate 8 ${ny} 1
replicate 8 8 1
orthogonal box = (0 0 -0.392) to (188.16 188.16 19.6)
4 by 4 by 1 MPI processor grid
36864 atoms
Time spent = 0.0028758 secs
# add adatoms
include adatoms.list.${add}
include adatoms.list.37K
create_atoms 1 single 27.5 9.5 4
Created 1 atoms
Time spent = 0.000183105 secs
create_atoms 1 single 16 9 4
Created 1 atoms
Time spent = 0.000178099 secs
create_atoms 1 single 10 12 4
Created 1 atoms
Time spent = 0.000179768 secs
create_atoms 1 single 31 44 4
Created 1 atoms
Time spent = 0.000184059 secs
create_atoms 1 single 13 17 4
Created 1 atoms
Time spent = 0.000173807 secs
create_atoms 1 single 8.5 28.5 4
Created 1 atoms
Time spent = 0.000167847 secs
create_atoms 1 single 23 26 4
Created 1 atoms
Time spent = 0.000179052 secs
create_atoms 1 single 38 27 4
Created 1 atoms
Time spent = 0.000169992 secs
create_atoms 1 single 37.5 4.5 4
Created 1 atoms
Time spent = 0.000166178 secs
create_atoms 1 single 41.5 47.5 4
Created 1 atoms
Time spent = 0.000172138 secs
create_atoms 1 single 20.5 37.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 5 8 4
Created 1 atoms
Time spent = 0.00018096 secs
create_atoms 1 single 2.5 16.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 38.5 45.5 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 9 0 4
Created 1 atoms
Time spent = 0.000168085 secs
create_atoms 1 single 39 32 4
Created 1 atoms
Time spent = 0.000170946 secs
create_atoms 1 single 45.5 11.5 4
Created 1 atoms
Time spent = 0.00018096 secs
create_atoms 1 single 40 0 4
Created 1 atoms
Time spent = 0.000168085 secs
create_atoms 1 single 44.5 2.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 4.5 44.5 4
Created 1 atoms
Time spent = 0.000168085 secs
create_atoms 1 single 24.5 13.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 47.5 23.5 4
Created 1 atoms
Time spent = 0.00018096 secs
create_atoms 1 single 1 20 4
Created 1 atoms
Time spent = 0.000166893 secs
create_atoms 1 single 38.5 31.5 4
Created 1 atoms
Time spent = 0.000168085 secs
create_atoms 1 single 12.5 12.5 4
Created 1 atoms
Time spent = 0.000169992 secs
create_atoms 1 single 2 27 4
Created 1 atoms
Time spent = 0.000188828 secs
create_atoms 1 single 21 5 4
Created 1 atoms
Time spent = 0.000174999 secs
create_atoms 1 single 47 12 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 32.5 46.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 9.5 40.5 4
Created 1 atoms
Time spent = 0.000166893 secs
create_atoms 1 single 8.5 2.5 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 41.5 22.5 4
Created 1 atoms
Time spent = 0.000174046 secs
create_atoms 1 single 29 11 4
Created 1 atoms
Time spent = 0.000166893 secs
create_atoms 1 single 3.5 3.5 4
Created 1 atoms
Time spent = 0.000165224 secs
create_atoms 1 single 5 21 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 46.5 31.5 4
Created 1 atoms
Time spent = 0.000166178 secs
create_atoms 1 single 35 46 4
Created 1 atoms
Time spent = 0.000183105 secs
create_atoms 1 single 40.5 41.5 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 10 22 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 43.5 14.5 4
Created 1 atoms
Time spent = 0.000169992 secs
create_atoms 1 single 42 42 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 4 26 4
Created 1 atoms
Time spent = 0.000174999 secs
create_atoms 1 single 19 34 4
Created 1 atoms
Time spent = 0.000163078 secs
create_atoms 1 single 33 9 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 0.5 45.5 4
Created 1 atoms
Time spent = 0.000163078 secs
create_atoms 1 single 30.5 32.5 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 25.5 5.5 4
Created 1 atoms
Time spent = 0.000178099 secs
create_atoms 1 single 47.5 39.5 4
Created 1 atoms
Time spent = 0.000165939 secs
create_atoms 1 single 15 13 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 21 21 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 14 28 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 9 34 4
Created 1 atoms
Time spent = 0.000174999 secs
create_atoms 1 single 7 38 4
Created 1 atoms
Time spent = 0.000175953 secs
create_atoms 1 single 11 35 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 20.5 45.5 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 30.5 31.5 4
Created 1 atoms
Time spent = 0.000159979 secs
create_atoms 1 single 32.5 2.5 4
Created 1 atoms
Time spent = 0.000166178 secs
create_atoms 1 single 21.5 3.5 4
Created 1 atoms
Time spent = 0.000157833 secs
create_atoms 1 single 23 12 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 4.5 33.5 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 46 43 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 42.5 45.5 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 4.5 10.5 4
Created 1 atoms
Time spent = 0.000158072 secs
create_atoms 1 single 33.5 15.5 4
Created 1 atoms
Time spent = 0.000157833 secs
create_atoms 1 single 24 5 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 13 16 4
Created 1 atoms
Time spent = 0.000158072 secs
create_atoms 1 single 16.5 23.5 4
Created 1 atoms
Time spent = 0.000156164 secs
create_atoms 1 single 45.5 28.5 4
Created 1 atoms
Time spent = 0.000247002 secs
create_atoms 1 single 44.5 5.5 4
Created 1 atoms
Time spent = 0.000156164 secs
create_atoms 1 single 27.5 46.5 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 44.5 12.5 4
Created 1 atoms
Time spent = 0.000157833 secs
create_atoms 1 single 12 41 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 6 4 4
Created 1 atoms
Time spent = 0.0001688 secs
create_atoms 1 single 31.5 10.5 4
Created 1 atoms
Time spent = 0.00015521 secs
create_atoms 1 single 1 44 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 31 4 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 21 33 4
Created 1 atoms
Time spent = 0.000156879 secs
create_atoms 1 single 3 33 4
Created 1 atoms
Time spent = 0.000164032 secs
create_atoms 1 single 15 10 4
Created 1 atoms
Time spent = 0.0001719 secs
create_atoms 1 single 28.5 22.5 4
Created 1 atoms
Time spent = 0.000153065 secs
create_atoms 1 single 43 1 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 3.5 0.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 41 37 4
Created 1 atoms
Time spent = 0.000153065 secs
create_atoms 1 single 18.5 43.5 4
Created 1 atoms
Time spent = 0.000213146 secs
create_atoms 1 single 17 27 4
Created 1 atoms
Time spent = 0.000159979 secs
create_atoms 1 single 3 5 4
Created 1 atoms
Time spent = 0.000153065 secs
create_atoms 1 single 18.5 23.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 31.5 14.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 41 31 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 22 3 4
Created 1 atoms
Time spent = 0.00015521 secs
create_atoms 1 single 14.5 40.5 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 9 38 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 36 42 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 33 22 4
Created 1 atoms
Time spent = 0.000163078 secs
create_atoms 1 single 15.5 47.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 3 0 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 25.5 27.5 4
Created 1 atoms
Time spent = 0.000176907 secs
create_atoms 1 single 2.5 28.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 29.5 28.5 4
Created 1 atoms
Time spent = 0.000162125 secs
create_atoms 1 single 44.5 18.5 4
Created 1 atoms
Time spent = 0.000152826 secs
create_atoms 1 single 26 40 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 41 27 4
Created 1 atoms
Time spent = 0.000158072 secs
create_atoms 1 single 39.5 5.5 4
Created 1 atoms
Time spent = 0.000155926 secs
create_atoms 1 single 3 38 4
Created 1 atoms
Time spent = 0.000152826 secs
create_atoms 1 single 35 29 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 11 19 4
Created 1 atoms
Time spent = 0.000164986 secs
create_atoms 1 single 18 1 4
Created 1 atoms
Time spent = 0.000146866 secs
create_atoms 1 single 39.5 40.5 4
Created 1 atoms
Time spent = 0.000146866 secs
create_atoms 1 single 46 17 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 1.5 23.5 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 28.5 23.5 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 10 28 4
Created 1 atoms
Time spent = 0.000159979 secs
create_atoms 1 single 19 47 4
Created 1 atoms
Time spent = 0.000148058 secs
create_atoms 1 single 10.5 16.5 4
Created 1 atoms
Time spent = 0.000147104 secs
create_atoms 1 single 38 45 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 42.5 41.5 4
Created 1 atoms
Time spent = 0.000161886 secs
create_atoms 1 single 47.5 42.5 4
Created 1 atoms
Time spent = 0.000147104 secs
create_atoms 1 single 38 7 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 10 44 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 29.5 27.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 45 30 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 3 9 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 8.5 35.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 24 44 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 47 4 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 7.5 8.5 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 32.5 41.5 4
Created 1 atoms
Time spent = 0.000157833 secs
create_atoms 1 single 0.5 34.5 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 11 8 4
Created 1 atoms
Time spent = 0.000147104 secs
create_atoms 1 single 2 40 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 25 24 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 47.5 6.5 4
Created 1 atoms
Time spent = 0.000147104 secs
create_atoms 1 single 39.5 28.5 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 17 21 4
Created 1 atoms
Time spent = 0.000164032 secs
create_atoms 1 single 32 43 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 16.5 29.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 34 34 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 11.5 3.5 4
Created 1 atoms
Time spent = 0.000154018 secs
create_atoms 1 single 39 22 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 24.5 36.5 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 33 31 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 35.5 35.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 14.5 34.5 4
Created 1 atoms
Time spent = 0.000146866 secs
create_atoms 1 single 34 28 4
Created 1 atoms
Time spent = 0.000153065 secs
create_atoms 1 single 37 41 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 33 46 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 27.5 28.5 4
Created 1 atoms
Time spent = 0.000145197 secs
create_atoms 1 single 40.5 22.5 4
Created 1 atoms
Time spent = 0.000150919 secs
create_atoms 1 single 27.5 1.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 12 2 4
Created 1 atoms
Time spent = 0.000151873 secs
create_atoms 1 single 36 43 4
Created 1 atoms
Time spent = 0.000144005 secs
create_atoms 1 single 28.5 9.5 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 20.5 25.5 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 3 3 4
Created 1 atoms
Time spent = 0.000144005 secs
create_atoms 1 single 38 33 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 3 20 4
Created 1 atoms
Time spent = 0.000154972 secs
create_atoms 1 single 35 11 4
Created 1 atoms
Time spent = 0.000145912 secs
create_atoms 1 single 5 25 4
Created 1 atoms
Time spent = 0.000144005 secs
create_atoms 1 single 36.5 6.5 4
Created 1 atoms
Time spent = 0.000144005 secs
create_atoms 1 single 19.5 24.5 4
Created 1 atoms
Time spent = 0.000236988 secs
create_atoms 1 single 27 41 4
Created 1 atoms
Time spent = 0.000169992 secs
create_atoms 1 single 39.5 11.5 4
Created 1 atoms
Time spent = 0.000138998 secs
create_atoms 1 single 21.5 2.5 4
Created 1 atoms
Time spent = 0.000136852 secs
create_atoms 1 single 46.5 15.5 4
Created 1 atoms
Time spent = 0.000138998 secs
create_atoms 1 single 13 24 4
Created 1 atoms
Time spent = 0.000137091 secs
create_atoms 1 single 11 37 4
Created 1 atoms
Time spent = 0.000144005 secs
create_atoms 1 single 11.5 31.5 4
Created 1 atoms
Time spent = 0.000144958 secs
create_atoms 1 single 47 0 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 25.5 17.5 4
Created 1 atoms
Time spent = 0.00014019 secs
create_atoms 1 single 32 11 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 8 17 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 27.5 12.5 4
Created 1 atoms
Time spent = 0.000137806 secs
create_atoms 1 single 25 7 4
Created 1 atoms
Time spent = 0.000146151 secs
create_atoms 1 single 25.5 37.5 4
Created 1 atoms
Time spent = 0.000139952 secs
create_atoms 1 single 12 15 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 1 7 4
Created 1 atoms
Time spent = 0.000138998 secs
create_atoms 1 single 18.5 47.5 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 5 38 4
Created 1 atoms
Time spent = 0.000136852 secs
create_atoms 1 single 42 19 4
Created 1 atoms
Time spent = 0.000149012 secs
create_atoms 1 single 30.5 7.5 4
Created 1 atoms
Time spent = 0.000138044 secs
create_atoms 1 single 42.5 7.5 4
Created 1 atoms
Time spent = 0.000138998 secs
create_atoms 1 single 26.5 18.5 4
Created 1 atoms
Time spent = 0.000153065 secs
create_atoms 1 single 18.5 1.5 4
Created 1 atoms
Time spent = 0.000137091 secs
create_atoms 1 single 41.5 10.5 4
Created 1 atoms
Time spent = 0.000140905 secs
# define frozen substrate and mobile atoms
region base block INF INF INF INF 0 1.8
set region base type 2
18432 settings made for type
group base type 2
18432 atoms in group base
group mobile type 1
18616 atoms in group mobile
# pair style
pair_style eam/alloy
pair_coeff * * ptvoterlammps.eam Pt Pt
neighbor 0.5 bin
neigh_modify every 1 delay 5 check yes
fix 1 mobile nve
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
fix 2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
fix 2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
fix 2 mobile langevin 400.0 400.0 1.0 826626413 zero yes
timestep 0.005
compute tmobile mobile temp
thermo 100
thermo_modify temp tmobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
# thermal equilibration
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.07583
ghost atom cutoff = 12
binsize = 3.03792, bins = 62 62 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.359 | 3.359 | 3.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -206220.22 0 -206220.22 -52155.664
100 188.18127 -206044.43 0 -205591.63 -25068.83
200 274.34464 -205860.78 0 -205200.66 -40191.797
300 325.66286 -205750.01 0 -204966.4 -31510.222
400 352.48242 -205675.42 0 -204827.28 -35058.064
500 370.88571 -205619.66 0 -204727.25 -32735.022
600 388.62129 -205592.87 0 -204657.78 -33904.556
700 389.54874 -205579.73 0 -204642.4 -32769.852
800 395.56074 -205576.82 0 -204625.03 -33755.948
900 398.03458 -205564.48 0 -204606.74 -32777.103
1000 401.24089 -205562.85 0 -204597.4 -33785.341
Loop time of 4.3687 on 16 procs for 1000 steps with 37048 atoms
Performance: 98.885 ns/day, 0.243 hours/ns, 228.901 timesteps/s
98.4% CPU use with 16 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2988 | 3.3828 | 3.4667 | 2.3 | 77.43
Neigh | 0.20856 | 0.23127 | 0.24382 | 1.9 | 5.29
Comm | 0.33313 | 0.45075 | 0.55485 | 9.2 | 10.32
Output | 0.00042987 | 0.00044042 | 0.00049591 | 0.0 | 0.01
Modify | 0.18811 | 0.28363 | 0.36798 | 9.7 | 6.49
Other | | 0.01983 | | | 0.45
Nlocal: 2315.5 ave 2332 max 2297 min
Histogram: 2 0 0 3 4 0 2 1 2 2
Nghost: 3186.31 ave 3205 max 3170 min
Histogram: 2 1 3 0 2 3 2 1 0 2
Neighs: 55590.9 ave 56174 max 55103 min
Histogram: 2 2 1 1 4 1 3 0 0 2
Total # of neighbors = 889454
Ave neighs/atom = 24.0082
Neighbor list builds = 105
Dangerous builds = 0
reset_timestep 0
# pin base so will not move during quenches
fix freeze base setforce 0.0 0.0 0.0
# event detection
compute event all event/displace ${cutevent}
compute event all event/displace 1.1
# hyper/local
fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
fix HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
fix HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
fix HL mobile hyper/local 3.2 0.3 0.4 ${Tequil} ${Dcut} ${alpha} ${boost}
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 ${Dcut} ${alpha} ${boost}
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 ${alpha} ${boost}
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 ${boost}
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 4000.0
# thermo output
thermo_style custom step temp pe f_HL f_HL[*]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
thermo_modify lost ignore
thermo_modify temp tmobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
thermo ${nevent}
thermo 100
# dump
region substrate block INF INF INF INF 1.8 3.8
region adatoms block INF INF INF INF 3.8 INF
variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
# run
hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
hyper 1500 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
hyper 1500 100 HL event min ${tol} ${tol} 1000 1000 dump 1
hyper 1500 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
hyper 1500 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.07583
ghost atom cutoff = 12
binsize = 3.03792, bins = 62 62 7
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix hyper/local, occasional
attributes: full, newton on, cut 10
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.566 | 7.567 | 7.567 Mbytes
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
0 401.24089 -205562.85 0 0 0 1 0 0 0 0 0 0 0 0 4e+19 0 0 0 0 0 0 0 0 0 0 0
77 401.24089 -206534.96 0 0 0 1 0 0 0 0 0 0 0 0 4e+19 0 0 0 0 0 0 0 1540 0 0 0
Loop time of 0.540347 on 16 procs for 77 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
0 401.24089 -205562.85 23.271302 74 0.18753621 1 6.0138739 703.62325 0 0.55802338 3.5350432 0 0 0 4e+19 10.115141 10.115141 0 0 0 0 0 0 0 0 0
100 399.15639 -205546.21 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
Loop time of 0.579085 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
100 399.15639 -205546.21 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
184 399.15639 -206534.96 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 49.934783 0.21714886 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 3680 0 0 0
Loop time of 0.556056 on 16 procs for 84 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
100 399.15639 -205546.21 22.903938 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
200 403.01717 -205543.17 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
Loop time of 0.581214 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
200 403.01717 -205543.17 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
275 403.01717 -206534.96 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 66.145455 0.29040418 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 5500 0 0 0
Loop time of 0.481812 on 16 procs for 75 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
200 403.01717 -205543.17 21.115577 91 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
300 399.01963 -205541.46 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
Loop time of 0.5757 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
300 399.01963 -205541.46 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
377 399.01963 -206534.96 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 73.225464 0.31760598 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 7540 0 0 0
Loop time of 0.514907 on 16 procs for 77 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
300 399.01963 -205541.46 19.137003 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
400 398.15351 -205544.87 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
Loop time of 0.577371 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
400 398.15351 -205544.87 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
471 398.15351 -206534.96 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 78.163482 0.33881076 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 9420 0 0 0
Loop time of 0.465473 on 16 procs for 71 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
400 398.15351 -205544.87 20.470689 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
500 400.29399 -205544.98 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0907861 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
Loop time of 0.579188 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
500 400.29399 -205544.98 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0907861 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
577 400.29399 -206534.96 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0910651 4.0779385 79.710572 0.3455768 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 11540 0 0 0
Loop time of 0.502193 on 16 procs for 77 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
500 400.29399 -205544.98 17.051107 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0910651 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
600 400.96099 -205544.56 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
Loop time of 0.694955 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
600 400.96099 -205544.56 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
680 400.96099 -206534.96 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 81.188235 0.35174818 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 13600 0 0 0
Loop time of 0.529041 on 16 procs for 80 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
600 400.96099 -205544.56 20.904088 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
700 397.78618 -205534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 1.1853748 4.1995704 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 0 0 0
Loop time of 0.590093 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
700 397.78618 -205534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 1.2139704 4.1995704 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 0 0 0
790 397.78618 -206534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 2.2107138 4.1995704 81.625316 0.35310868 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 15800 0 0 0
Loop time of 0.594281 on 16 procs for 90 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
700 397.78618 -205534.96 20.236364 94 0.51088027 0.39757442 6.0138739 703.62325 0.061146951 2.2107138 4.205089 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 1 2 6
800 399.66919 -205547.44 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.2107138 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 1 2 6
Loop time of 0.583824 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
800 399.66919 -205547.44 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.2107138 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 1 2 6
872 399.66919 -206535.54 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.3177682 4.3041291 84.739679 0.36548679 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 17440 1 2 6
Loop time of 0.46886 on 16 procs for 72 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
800 399.66919 -205547.44 21.2852 94 0.44964213 0.39739855 6.0138739 703.62325 0.06556778 2.3177682 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 2 4 13
900 401.5853 -205544.22 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
Loop time of 0.585137 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
900 401.5853 -205544.22 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
975 401.5853 -206535.54 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 84.939487 0.36762438 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 19500 2 4 13
Loop time of 0.502012 on 16 procs for 75 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
900 401.5853 -205544.22 19.307938 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
1000 395.06218 -205526.35 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
Loop time of 0.588597 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1000 395.06218 -205526.35 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
1083 395.06218 -206535.54 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 85.421053 0.36763584 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 21660 2 4 13
Loop time of 0.543222 on 16 procs for 83 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1000 395.06218 -205526.35 17.514191 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
1100 400.04484 -205545.92 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 2 4 13
Loop time of 0.590075 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1100 400.04484 -205545.92 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 2 4 13
1177 400.04484 -206535.53 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 86.464741 0.37201529 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 23540 2 4 13
Loop time of 0.500839 on 16 procs for 77 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1100 400.04484 -205545.92 19.518413 89 0.429675 0.39705701 6.0137119 703.6043 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 3 6 19
1200 400.7462 -205543.2 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
Loop time of 0.583971 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1200 400.7462 -205543.2 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
1277 400.7462 -206535.53 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 86.806578 0.37396584 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 25540 3 6 19
Loop time of 0.509118 on 16 procs for 77 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1200 400.7462 -205543.2 21.169281 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
1300 398.53702 -205539.33 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
Loop time of 0.587306 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1300 398.53702 -205539.33 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
1375 398.53702 -206535.53 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 87.455273 0.37616341 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 27500 3 6 19
Loop time of 0.483781 on 16 procs for 75 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1300 398.53702 -205539.33 21.35787 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
1400 402.80537 -205549.3 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
Loop time of 0.586411 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1400 402.80537 -205549.3 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
1471 402.80537 -206535.53 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 88.193746 0.37856948 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 29420 3 6 19
Loop time of 0.473799 on 16 procs for 71 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1400 402.80537 -205549.3 19.481632 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
1500 402.0803 -205537.7 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 92.857333 0.39767858 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 30000 3 6 19
Loop time of 0.587342 on 16 procs for 100 steps with 37048 atoms
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
1500 402.0803 -205537.7 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 92.857333 0.39767858 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 30000 3 6 19
1574 402.0803 -206535.53 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 88.491741 0.37898213 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 31480 3 6 19
Loop time of 0.493982 on 16 procs for 74 steps with 37048 atoms
Final hyper stats ...
Cummulative quantities for fix hyper:
hyper time = 30000
event timesteps = 3
# of atoms in events = 6
Quantities for this hyper run:
event timesteps = 3
# of atoms in events = 6
max length of any bond = 4.4266
max drift distance of any atom = 2.31777
fraction of steps & bonds with zero bias = 0.0704091
Current quantities:
ave bonds/atom = 6.01371
Cummulative quantities specific tofix hyper/local:
# of new bonds formed = 19
max bonds/atom = 13
Quantities for this hyper run specific to fix hyper/local:
ave boosted bonds/step = 92.8573
ave boost coeff of all bonds = 0.397679
max boost coeff of any bond = 0.414894
min boost coeff of any bond = 0.383728
max dist from my box of any non-maxstrain bond ghost atom = 10.333
max dist from my box of any bond ghost atom = 10.3858
count of ghost bond neighbors not found on reneighbor steps = 0
lost bond partners = 0
ave bias coeff for lost bond partners = 0
bias overlaps = 0
non-matching bias coeffs = 0
CPU time for bond builds = 0.044807
Current quantities specific to fix hyper/local:
neighbor bonds/bond = 703.604
ave boost coeff for all bonds = 0.396356
Loop time of 17.9972 on 16 procs for 1500 steps with 37048 atoms
Performance: 36.006 ns/day, 0.667 hours/ns, 83.346 timesteps/s
120.7% CPU use with 16 MPI tasks x no OpenMP threads
Hyper stats:
Dynamics time (%) = 8.87027 (49.2869)
Quench time (%) = 8.15972 (45.3388)
Other time (%) = 1.2212 (6.78552)
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.6 | 11.848 | 12.043 | 3.9 | 65.83
Neigh | 0.50025 | 0.52638 | 0.55163 | 2.1 | 2.92
Comm | 0.34528 | 0.49905 | 0.66742 | 13.3 | 2.77
Output | 0.0021305 | 0.0021461 | 0.0022686 | 0.1 | 0.01
Modify | 3.7498 | 3.9009 | 3.9786 | 2.8 | 21.67
Other | | 1.221 | | | 6.79
Nlocal: 2315.5 ave 2361 max 2267 min
Histogram: 1 1 0 4 2 1 3 3 0 1
Nghost: 3187.88 ave 3236 max 3141 min
Histogram: 1 0 3 2 2 1 4 1 1 1
Neighs: 53950.6 ave 54989 max 53049 min
Histogram: 2 0 3 2 1 2 4 1 0 1
FullNghs: 542951 ave 554654 max 533224 min
Histogram: 1 2 3 1 2 2 2 2 0 1
Total # of neighbors = 8687214
Ave neighs/atom = 234.485
Neighbor list builds = 165
Dangerous builds = 0
Total wall time: 0:00:22

1250
examples/hyper/log.25Mar19.hyper.global.g++.4 Normal file
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examples/hyper/log.25Mar19.hyper.local.g++.16 Normal file
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# example for performing a query to the OpenKIM test database to retrieve
# a parameter to be used in the input. here it requests the aluminium
# lattice constant for a specific test used for a specific model and then
# assigns it to the variable 'latconst'
units metal
info variables out log
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
info variables out log
lattice fcc ${latconst}

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