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lammps
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Merge with current master

This commit is contained in:
mkanski 2019-04-03 19:17:15 +02:00
parent d7a5bf4e16 f73ccc3025
commit 501558743b
831 changed files with 15054 additions and 8897 deletions
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6
.github/PULL_REQUEST_TEMPLATE.md vendored
View File

@ -4,7 +4,7 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
**Related Issues**
__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
**Author(s)**
@ -16,7 +16,7 @@ By submitting this pull request, I agree, that my contribution will be included
**Backward Compatibility**
_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
**Implementation Notes**
@ -24,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
**Post Submission Checklist**
_Please check the fields below as they are completed **after** the pull request has been submitted_
_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
- [ ] The feature or features in this pull request is complete
- [ ] Licensing information is complete

280
cmake/CMakeLists.txt
View File

@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
find_package(Git)
# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
# this is fast, so check for it all the time
message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@ -205,7 +207,7 @@ include_directories(${LAMMPS_SOURCE_DIR})
if(PKG_USER-ADIOS)
# The search for ADIOS2 must come before MPI because
# it includes its own MPI search with the latest FindMPI.cmake
# script that defines the MPI::MPI_C target
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
@ -320,7 +322,7 @@ pkg_depends(USER-SCAFACOS MPI)
find_package(OpenMP QUIET)
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
@ -379,19 +381,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
endif()
if(PKG_PYTHON)
find_package(PythonInterp REQUIRED)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
include_directories(${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)
@ -567,6 +560,20 @@ if(PKG_USER-PLUMED)
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
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
@ -575,9 +582,11 @@ if(PKG_USER-PLUMED)
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 ${INSTALL_DIR})
@ -611,9 +620,13 @@ if(PKG_USER-PLUMED)
endif()
if(PKG_USER-MOLFILE)
set(MOLFILE_INCLUDE_DIRS "${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 ${CMAKE_DL_LIBS})
endif()
list(APPEND LAMMPS_LINK_LIBS molfile)
endif()
@ -624,7 +637,6 @@ if(PKG_USER-NETCDF)
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
if(PKG_USER-SMD)
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
if(DOWNLOAD_EIGEN3)
@ -668,15 +680,21 @@ if(PKG_USER-VTK)
endif()
if(PKG_KIM)
option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
find_package(CURL)
if(CURL_FOUND)
include_directories(${CURL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
add_definitions(-DLMP_KIM_CURL)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)
if(DOWNLOAD_KIM)
message(STATUS "KIM-API v2 download requested - we will build our own")
message(STATUS "KIM-API download requested - we will build our own")
enable_language(C)
enable_language(Fortran)
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
URL_MD5 537d9c0abd30f85b875ebb584f9143fa
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@ -685,17 +703,17 @@ if(PKG_KIM)
-DCMAKE_BUILD_TYPE=${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${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM-API-V2)
if(NOT KIM-API-V2_FOUND)
message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
find_package(KIM-API)
if(NOT KIM-API_FOUND)
message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS "${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)
@ -710,6 +728,7 @@ if(PKG_MESSAGE)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
@ -945,7 +964,7 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${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)
@ -1058,37 +1077,79 @@ 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()
@ -1101,33 +1162,33 @@ 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)
@ -1169,6 +1230,10 @@ 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)")
@ -1232,7 +1297,7 @@ 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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@ -1326,6 +1391,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
######################################
# Generate 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
############################################
@ -1447,6 +1524,49 @@ 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
#

22
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 +28,23 @@
# 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)
include(FindPackageHandleStandardArgs)
pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
pkg_check_modules(KIM-API REQUIRED 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)
pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
# 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>

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)

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()

18
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)/ ;\
@ -135,14 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
make && \
make && \
mv LAMMPS.pdf ../Manual.pdf && \
cd ../;
@(\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ../../; \
)
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;\
)

8
doc/src/Build_cmake.txt
View File

@ -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.

91
doc/src/Build_extras.txt
View File

@ -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:
@ -169,26 +171,24 @@ 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/kim-items/model-drivers/alphabetical
https://openkim.org/browse/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
https://openkim.org/kim-api on the "What is in the KIM API source
package?" page.
https://openkim.org/browse/models/by-model-drivers
[CMake build]:
@ -197,7 +197,7 @@ package?" page.
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]:
@ -859,23 +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:
@ -897,7 +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]:
@ -906,7 +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

37
doc/src/Build_package.txt
View File

@ -149,26 +149,39 @@ 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/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
View File

@ -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
View File

@ -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,

2
doc/src/Commands_fix.txt
View File

@ -224,7 +224,7 @@ 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
View File

@ -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}

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

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.

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

6
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

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

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

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

3
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
@ -578,6 +580,7 @@ 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

17
doc/src/pair_kim.txt
View File

@ -31,14 +31,10 @@ element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file.
See the current list of "KIM model
drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
drivers"_https://openkim.org/browse/model-drivers/alphabetical.
See the current list of all "KIM
models"_https://openkim.org/kim-items/models/by-model-drivers
See the list of "example KIM models"_https://openkim.org/kim-api which
are included in the KIM library by default, in the "What is in the KIM
API source package?" section.
models"_https://openkim.org/browse/models/by-model-drivers
To use this pair style, you must first download and install the KIM
API library from the "OpenKIM website"_https://openkim.org. The KIM
@ -46,12 +42,9 @@ 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
The argument {model} is the name of the KIM model for a specific

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

26
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
@ -346,6 +349,7 @@ Cij
cis
civ
clearstore
Cleary
Clebsch
clemson
Clermont
@ -372,6 +376,7 @@ Coeff
CoefficientN
coeffs
Coeffs
cohesionless
Coker
Colberg
coleman
@ -449,6 +454,7 @@ cuda
Cuda
CUDA
CuH
Cummins
Curk
customIDs
cutbond
@ -492,6 +498,7 @@ darkturquoise
darkviolet
Das
Dasgupta
dashpot
dat
datafile
datums
@ -529,6 +536,7 @@ Dequidt
der
derekt
Derjagin
Derjaguin
Derlet
Deserno
Destree
@ -627,6 +635,7 @@ dVx
dW
dx
dy
dylib
dyn
dyne
dynes
@ -1079,6 +1088,7 @@ Hyoungki
hyperdynamics
hyperradius
hyperspherical
hysteretic
Ibanez
ibar
ibm
@ -1138,6 +1148,7 @@ interconvert
interial
interlayer
intermolecular
Interparticle
interstitials
Intr
intra
@ -1156,6 +1167,7 @@ IPython
Isele
isenthalpic
ish
Ishida
iso
isodemic
isoenergetic
@ -1265,6 +1277,7 @@ kcl
Kd
KDevelop
ke
kepler
KE
Keblinski
keflag
@ -1298,6 +1311,7 @@ Kondor
konglt
Koning
Kooser
Korn
Koskinen
Koster
Kosztin
@ -1382,6 +1396,7 @@ libAtoms
libawpmd
libch
libcolvars
libcurl
libdir
libdl
libfftw
@ -1449,6 +1464,7 @@ logfile
logfreq
logicals
Lomdahl
Lond
lookups
Lookups
LoopVar
@ -1464,6 +1480,7 @@ lsfftw
ltbbmalloc
lubricateU
lucy
Luding
Lussetti
Lustig
lwsock
@ -1502,6 +1519,7 @@ manybody
MANYBODY
Maras
Marrink
Marroquin
Marsaglia
Marseille
Martyna
@ -1513,6 +1531,7 @@ masstotal
Masuhiro
Matchett
Materias
mathbf
matlab
matplotlib
Mattox
@ -1601,6 +1620,7 @@ Mie
Mikami
Militzer
Minary
Mindlin
mincap
mingw
minima
@ -1671,6 +1691,7 @@ mpiexec
mpiio
mpirun
mplayer
mps
Mryglod
mscg
MSCG
@ -1954,6 +1975,7 @@ oneway
onn
ons
OO
opencl
openKIM
OpenMP
openmp
@ -2286,6 +2308,7 @@ rg
Rg
Rhaphson
rheological
rheology
rhodo
Rhodo
rhodopsin
@ -2602,6 +2625,7 @@ Tait
taitwater
Tajkhorshid
Tamaskovics
Tanaka
tanh
Tartakovsky
taskset
@ -2689,6 +2713,7 @@ tokyo
tol
toolchain
topologies
Toporov
Torder
torsions
Tosi
@ -2733,6 +2758,7 @@ Tsrd
Tstart
tstat
Tstop
Tsuji
Tsuzuki
tt
Tt

55
examples/SPIN/spinmin/in.spinmin.bfo Normal file
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@ -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
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@ -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

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6
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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993
examples/hyper/log.10Oct18.hyper.local.g++.16
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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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1002
examples/hyper/log.25Mar19.hyper.local.g++.16 Normal file
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11
examples/kim/in.query Normal file
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@ -0,0 +1,11 @@
# 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}

34
examples/kim/log.22Mar2019.query.g++.1 Normal file
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@ -0,0 +1,34 @@
LAMMPS (28 Feb 2019)
# 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
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:56 2019
Variable information:
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
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
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:57 2019
Variable information:
Variable[ 0]: latconst , style = string , def = 4.03208274841
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
lattice fcc ${latconst}
lattice fcc 4.03208274841
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
Total wall time: 0:00:00

12
examples/micelle/data.micelle
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@ -49,7 +49,7 @@
22 0 1 25.100 0.000 0.000
23 0 1 26.295 0.000 0.000
24 110 2 27.490 0.000 0.000
25 128 2 28.685 0.000 0.000
25 128 2 28.685 35.85686 0.000
26 0 1 29.881 0.000 0.000
27 0 1 31.076 0.000 0.000
28 0 1 32.271 0.000 0.000
@ -175,7 +175,7 @@
148 0 1 32.271 4.781 0.000
149 0 1 33.466 4.781 0.000
150 0 1 34.662 4.781 0.000
151 53 2 0.000 5.976 0.000
151 53 2 35.85686 5.976 0.000
152 0 1 1.195 5.976 0.000
153 0 1 2.390 5.976 0.000
154 0 1 3.586 5.976 0.000
@ -655,7 +655,7 @@
628 0 1 32.271 23.905 0.000
629 0 1 33.466 23.905 0.000
630 0 1 34.662 23.905 0.000
631 148 2 0.000 25.100 0.000
631 148 2 35.85686 25.100 0.000
632 0 1 1.195 25.100 0.000
633 0 1 2.390 25.100 0.000
634 0 1 3.586 25.100 0.000
@ -976,7 +976,7 @@
949 25 3 0.677 33.143 0.000
950 25 4 1.353 32.819 0.000
951 26 3 35.071 18.557 0.000
952 26 4 35.480 19.186 0.000
952 26 4 35.48000 19.186 0.000
953 27 3 29.131 15.504 0.000
954 27 4 28.382 15.470 0.000
955 28 3 23.456 33.395 0.000
@ -1096,7 +1096,7 @@
1069 85 3 33.021 33.461 0.000
1070 85 4 33.771 33.455 0.000
1071 86 3 0.552 18.315 0.000
1072 86 4 35.766 18.701 0.000
1072 86 4 -0.09086 18.701 0.000
1073 87 3 28.026 32.796 0.000
1074 87 4 28.562 33.321 0.000
1075 88 3 24.351 29.925 0.000
@ -1112,7 +1112,7 @@
1085 93 3 26.170 16.278 0.000
1086 93 4 26.046 17.017 0.000
1087 94 3 10.380 0.547 0.000
1088 94 4 10.003 35.755 0.000
1088 94 4 10.003 -0.10186 0.000
1089 95 3 0.419 29.308 0.000
1090 95 4 0.837 29.930 0.000
1091 96 3 13.712 28.191 0.000

4
examples/micelle/in.micelle
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@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
thermo 50
#dump 1 all atom 2000 dump.micelle
@ -69,4 +69,4 @@ thermo 1000
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
run 1000

87
examples/micelle/in.micelle-rigid Normal file
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@ -0,0 +1,87 @@
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
special_bonds fene
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
group solute subtract all solvent
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 500
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
fix 4 all enforce2d
run 500

86
examples/micelle/in.micelle.rigid Normal file
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@ -0,0 +1,86 @@
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
special_bonds fene
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
group solute subtract all solvent
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000

255
examples/micelle/log.27Nov18.micelle.g++.1
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@ -1,255 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
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 = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms
Performance: 2582728.958 tau/day, 5978.539 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
Other | | 0.006227 | | | 3.72
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298
2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
Performance: 1859917.639 tau/day, 4305.365 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 | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
Other | | 0.3493 | | | 2.51
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 405 ave 405 max 405 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9565 ave 9565 max 9565 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9565
Ave neighs/atom = 7.97083
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0
Total wall time: 0:00:14

255
examples/micelle/log.27Nov18.micelle.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
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 = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms
Performance: 6729792.131 tau/day, 15578.223 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
Other | | 0.003891 | | | 6.06
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402
2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
Performance: 5681397.232 tau/day, 13151.382 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
Other | | 0.2346 | | | 5.14
Nlocal: 300 ave 306 max 289 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 227.25 ave 250 max 216 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 2373.25 ave 2489 max 2283 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 9493
Ave neighs/atom = 7.91083
Ave special neighs/atom = 0.5
Neighbor list builds = 4888
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000473022 secs
read_data CPU = 0.0024147 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00022316 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
Performance: 2093802.885 tau/day, 4846.766 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21
Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11
Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86
Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17
Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37
Other | | 0.002726 | | | 2.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3094 ave 3094 max 3094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
Performance: 1208012.705 tau/day, 2796.326 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17
Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38
Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92
Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45
Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10
Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34
Other | | 0.00293 | | | 1.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 416 ave 416 max 416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8769 ave 8769 max 8769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.00015378 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
Performance: 1297278.008 tau/day, 3002.958 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51
Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56
Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83
Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44
Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11
Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66
Other | | 0.003141 | | | 1.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8743 ave 8743 max 8743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000422001 secs
read_data CPU = 0.00473404 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000183344 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
Performance: 5066547.720 tau/day, 11728.120 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
Other | | 0.002669 | | | 6.26
Nlocal: 300 ave 304 max 292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 103.5 ave 108 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 773.5 ave 792 max 735 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 500
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
Performance: 2434100.210 tau/day, 5634.491 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
Other | | 0.002938 | | | 3.31
Nlocal: 300 ave 309 max 291 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 218.75 ave 223 max 216 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 2192.25 ave 2251 max 2113 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 7.70092e-05 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
Performance: 3671840.233 tau/day, 8499.630 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
Other | | 0.00224 | | | 3.81
Nlocal: 300 ave 303 max 295 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 219 ave 224 max 215 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2185.75 ave 2244 max 2143 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

218
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LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00037837 secs
read_data CPU = 0.00206876 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000177383 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
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 = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms
Performance: 2068027.282 tau/day, 4787.100 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70
Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04
Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31
Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76
Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17
Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35
Other | | 0.00558 | | | 2.67
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
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 = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022
600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405
650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263
700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923
750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254
800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696
850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879
900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909
950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421
1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315
Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms
Performance: 1712557.882 tau/day, 3964.254 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09
Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35
Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82
Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95
Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15
Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38
Other | | 0.005685 | | | 2.25
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8586 ave 8586 max 8586 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

218
examples/micelle/log.29Mar2019.micelle.g++.4 Normal file
View File

@ -0,0 +1,218 @@
LAMMPS (29 Mar 2019)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000413656 secs
read_data CPU = 0.00487924 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000178576 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
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 = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms
Performance: 4766906.584 tau/day, 11034.506 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33
Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70
Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85
Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53
Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68
Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19
Other | | 0.006081 | | | 6.71
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 50
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
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 = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023
600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405
650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262
700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692
750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235
800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703
850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884
900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008
950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854
1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447
Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
Performance: 4917357.613 tau/day, 11382.772 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60
Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54
Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04
Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79
Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74
Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11
Other | | 0.00455 | | | 5.18
Nlocal: 300 ave 305 max 296 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 219.5 ave 228 max 214 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 2146.5 ave 2201 max 2114 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

2
lib/gpu/lal_device.cpp
View File

@ -237,7 +237,7 @@ int DeviceT::set_ocl_params(char *ocl_vendor) {
" -DBLOCK_CELL_ID="+params[11]+
" -DMAX_BIO_SHARED_TYPES="+params[12];
}
_ocl_compile_string="-cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
_ocl_compile_string="-cl-std=CL1.2 -cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
std::string(OCL_PRECISION_COMPILE)+" "+_ocl_vendor_string;
#endif
return 0;

10
lib/kim/Install.py
View File

@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
# settings
thisdir = fullpath('.')
version = "kim-api-v2-2.0.1"
version = "kim-api-2.0.2"
# help message
@ -40,10 +40,10 @@ make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver
See the list of KIM model drivers here:
https://openkim.org/kim-items/model-drivers/alphabetical
https://openkim.org/browse/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
https://openkim.org/browse/models/by-model-drivers
"""
pgroup = parser.add_mutually_exclusive_group()
@ -154,7 +154,7 @@ if buildflag:
# add all OpenKIM models, if desired
if everythingflag:
print("Adding all OpenKIM models, this will take a while ...")
cmd = '%s/bin/kim-api-v2-collections-management install system OpenKIM' % (kimdir)
cmd = '%s/bin/kim-api-collections-management install system OpenKIM' % (kimdir)
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
if verboseflag:
print(txt.decode("UTF-8"))
@ -171,7 +171,7 @@ if addflag:
sys.exit("\nkim-api is not installed")
# download single model
cmd = '%s/bin/kim-api-v2-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
cmd = '%s/bin/kim-api-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
if verboseflag:
print(txt.decode("UTF-8"))

11
lib/kim/Makefile.lammps
View File

@ -17,13 +17,18 @@
ifeq ($(strip $(shell pkg-config --version)),)
$(error 'pkg-config' not found, but is required to configure the KIM API)
endif
kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null)
# there is no usable libcurl installation
ifeq ($(shell curl-config --version 2> /dev/null),)
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api 2> /dev/null)
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api 2> /dev/null)
else
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api 2> /dev/null) $(shell curl-config --libs)
endif
ifeq ($(strip $(kim_SYSINC)),)
$(error 'pkg-config' could not find an installed KIM API library.)

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