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Merge from lammps master

This commit is contained in:
julient31 2018-05-21 16:06:53 -06:00
parent 437e854741 94c6d2d546
commit 1641f78e3e
1621 changed files with 28923 additions and 7380 deletions
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36
.github/CODEOWNERS vendored
View File

@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1
lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey
lib/vtk/* @rbberger
lib/kim/* @ellio167
# packages
src/KOKKOS @stanmoore1
src/USER-CGSDK @akohlmey
src/USER-COLVARS @giacomofiorin
src/USER-OMP @akohlmey
src/USER-QMMM @akohlmey
# whole packages
src/COMPRESS/* @akohlmey
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-DPD/* @timattox
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MEAMC/* @martok
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PHONON/* @lingtikong
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
src/USER-VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/USER-MISC/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
# tools
tools/msi2lmp/* @akohlmey

318
cmake/CMakeLists.txt
View File

@ -4,7 +4,7 @@
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.1)
project(lammps)
project(lammps LANGUAGES CXX)
set(SOVERSION 0)
set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
@ -23,14 +23,22 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
# remove any style headers in the src dir
file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
if(SRC_STYLE_FILES)
file(REMOVE ${SRC_STYLE_FILES})
file(GLOB SRC_FILES ${LAMMPS_SOURCE_DIR}/*.cpp)
list(SORT SRC_FILES)
# check for files installed by make-based buildsystem
# only run this time consuming check if there are new files
if(NOT SRC_FILES STREQUAL SRC_FILES_CACHED)
file(GLOB SRC_PKG_FILES ${LAMMPS_SOURCE_DIR}/*/*.cpp)
message(STATUS "Running check for installed package (this might take a while)")
foreach(_SRC SRC_PKG_FILES)
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
message(FATAL_ERROR "Found packages installed by the make-based buildsystem, please run 'make -C ${LAMMPS_SOURCE_DIR} no-all purge'")
endif()
endforeach()
set(SRC_FILES_CACHED "${SRC_FILES}" CACHE INTERNAL "List of file in LAMMPS_SOURCE_DIR" FORCE)
endif()
enable_language(CXX)
######################################################################
# compiler tests
# these need ot be done early (before further tests).
@ -48,21 +56,27 @@ option(BUILD_SHARED_LIBS "Build shared libs" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
option(DEVELOPER_MODE "Enable developer mode" OFF)
mark_as_advanced(DEVELOPER_MODE)
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
include(GNUInstallDirs)
set(LAMMPS_LINK_LIBS)
set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
option(ENABLE_MPI "Build MPI version" OFF)
if(ENABLE_MPI)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI)
find_package(MPI REQUIRED)
include_directories(${MPI_C_INCLUDE_PATH})
include_directories(${MPI_CXX_INCLUDE_PATH})
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
endif()
else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
@ -101,21 +115,21 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
REAX REPLICA RIGID SHOCK SNAP SRD)
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
USER-ATC USER-AWPMD USER-CGDNA USER-MESO
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES})
option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
endforeach()
foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
macro(pkg_depends PKG1 PKG2)
if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
if(PKG_${PKG1} AND NOT PKG_${PKG2})
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
endif()
endmacro()
@ -128,38 +142,53 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-MISC MANYBODY)
pkg_depends(USER-PHONON KSPACE)
if(ENABLE_BODY AND ENABLE_POEMS)
message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
endif()
######################################################
# packages with special compiler needs or external libs
######################################################
if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
enable_language(Fortran)
include(CheckFortranCompilerFlag)
check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
endif()
if(ENABLE_KOKKOS OR ENABLE_MSCG)
if(PKG_MEAM)
enable_language(C)
endif()
if(PKG_KOKKOS OR PKG_MSCG)
# starting with CMake 3.1 this is all you have to do to enforce C++11
set(CMAKE_CXX_STANDARD 11) # C++11...
set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
endif()
if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
find_package(OpenMP QUIET)
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
find_package(OpenMP REQUIRED)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
if(ENABLE_KSPACE)
set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
if(PKG_KSPACE)
option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
set(FFTW "FFTW3")
if(FFT_SINGLE)
set(FFTW "FFTW3F")
add_definitions(-DFFT_SINGLE)
endif()
find_package(${FFTW} QUIET)
if(${FFTW}_FOUND)
set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
else()
set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
endif()
set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL)
if(NOT FFT STREQUAL "KISSFFT")
find_package(${FFT} REQUIRED)
add_definitions(-DFFT_${FFT})
if(NOT FFT STREQUAL "FFTW3F")
add_definitions(-DFFT_FFTW)
else()
add_definitions(-DFFT_${FFT})
endif()
include_directories(${${FFT}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
endif()
@ -170,22 +199,17 @@ if(ENABLE_KSPACE)
endif()
endif()
if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
if(NOT LAPACK_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
add_library(linalg STATIC ${LAPACK_SOURCES})
include(CheckFortranCompilerFlag)
check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
if(FC_HAS_NO_SECOND_UNDERSCORE)
target_compile_options(linalg PRIVATE -fno-second-underscore)
endif()
set(LAPACK_LIBRARIES linalg)
endif()
endif()
if(ENABLE_PYTHON)
if(PKG_PYTHON)
find_package(PythonInterp REQUIRED)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
@ -201,16 +225,25 @@ if(ENABLE_PYTHON)
endif()
endif()
find_package(JPEG)
if(JPEG_FOUND)
find_package(JPEG QUIET)
option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
if(WITH_JPEG)
find_package(JPEG REQUIRED)
add_definitions(-DLAMMPS_JPEG)
include_directories(${JPEG_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
endif()
find_package(PNG)
find_package(ZLIB)
find_package(PNG QUIET)
find_package(ZLIB QUIET)
if(PNG_FOUND AND ZLIB_FOUND)
option(WITH_PNG "Enable PNG support" ON)
else()
option(WITH_PNG "Enable PNG support" OFF)
endif()
if(WITH_PNG)
find_package(PNG REQUIRED)
find_package(ZLIB REQUIRED)
include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
add_definitions(-DLAMMPS_PNG)
@ -218,25 +251,50 @@ endif()
find_program(GZIP_EXECUTABLE gzip)
find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
if(GZIP_FOUND)
option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
if(WITH_GZIP)
if(NOT GZIP_FOUND)
message(FATAL_ERROR "gzip executable not found")
endif()
add_definitions(-DLAMMPS_GZIP)
endif()
find_program(FFMPEG_EXECUTABLE ffmpeg)
find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
if(FFMPEG_FOUND)
option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
if(WITH_FFMPEG)
if(NOT FFMPEG_FOUND)
message(FATAL_ERROR "ffmpeg executable not found")
endif()
add_definitions(-DLAMMPS_FFMPEG)
endif()
if(ENABLE_VORONOI)
find_package(VORO REQUIRED) #some distros
if(PKG_VORONOI)
option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
if(DOWNLOAD_VORO)
include(ExternalProject)
ExternalProject_Add(voro_build
URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
)
ExternalProject_get_property(voro_build SOURCE_DIR)
set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
list(APPEND LAMMPS_DEPS voro_build)
else()
find_package(VORO)
if(NOT VORO_FOUND)
message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
endif()
include_directories(${VORO_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
endif()
if(ENABLE_LATTE)
find_package(LATTE QUIET)
if(NOT LATTE_FOUND)
if(PKG_LATTE)
option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
if(DOWNLOAD_LATTE)
message(STATUS "LATTE not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
@ -248,55 +306,79 @@ if(ENABLE_LATTE)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
list(APPEND LAMMPS_DEPS latte_build)
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
if(ENABLE_USER-MOLFILE)
if(PKG_USER-MOLFILE)
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
list(APPEND LAMMPS_LINK_LIBS molfile)
endif()
if(ENABLE_USER-NETCDF)
if(PKG_USER-NETCDF)
find_package(NetCDF REQUIRED)
include_directories(NETCDF_INCLUDE_DIR)
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
if(ENABLE_USER-SMD)
find_package(Eigen3 REQUIRED)
if(PKG_USER-SMD)
option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
if(DOWNLOAD_Eigen3)
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
URL_MD5 1a47e78efe365a97de0c022d127607c3
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DEIGEN_TEST_NOQT=ON
-DCMAKE_DISABLE_FIND_PACKAGE_LAPACK=ON -DCMAKE_DISABLE_FIND_PACKAGE_Cholmod=ON -DCMAKE_DISABLE_FIND_PACKAGE_Umfpack=ON -DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=ON
-DCMAKE_DISABLE_FIND_PACKAGE_PASTIX=ON -DCMAKE_DISABLE_FIND_PACKAGE_SPQR=ON -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON -DCMAKE_DISABLE_FIND_PACKAGE_CUDA=ON
-DCMAKE_DISABLE_FIND_PACKAGE_FFTW=ON -DCMAKE_DISABLE_FIND_PACKAGE_MPFR=ON -DCMAKE_DISABLE_FIND_PACKAGE_OpenGL=ON
)
ExternalProject_get_property(Eigen3_build INSTALL_DIR)
set(EIGEN3_INCLUDE_DIR ${INSTALL_DIR}/include/eigen3)
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3)
if(NOT Eigen3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
endif()
endif()
include_directories(${EIGEN3_INCLUDE_DIR})
endif()
if(ENABLE_USER-QUIP)
if(PKG_USER-QUIP)
find_package(QUIP REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
if(ENABLE_USER-QMMM)
if(PKG_USER-QMMM)
message(WARNING "Building QMMM with CMake is still experimental")
find_package(QE REQUIRED)
include_directories(${QE_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
if(ENABLE_USER-VTK)
if(PKG_USER-VTK)
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
add_definitions(-DLAMMPS_VTK)
list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
endif()
if(ENABLE_KIM)
find_package(KIM QUIET)
if(NOT KIM_FOUND)
message(STATUS "KIM not found - we will build our own")
if(PKG_KIM)
option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
if(DOWNLOAD_KIM)
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
URL_MD5 9f66efc128da33039e30659f36fc6d00
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
)
@ -304,12 +386,17 @@ if(ENABLE_KIM)
set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM)
if(NOT KIM_FOUND)
message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
include_directories(${KIM_INCLUDE_DIRS})
endif()
if(ENABLE_MSCG)
if(PKG_MSCG)
find_package(GSL REQUIRED)
set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
@ -333,12 +420,18 @@ if(ENABLE_MSCG)
target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
if(PKG_COMPRESS)
find_package(ZLIB REQUIRED)
include_directories(${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFile)
include(CheckIncludeFileCXX)
foreach(HEADER math.h)
check_include_file(${HEADER} FOUND_${HEADER})
check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
endif(NOT FOUND_${HEADER})
@ -382,7 +475,7 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
endforeach()
if(ENABLE_${PKG})
if(PKG_${PKG})
# detects styles in package and adds them to global list
RegisterStyles(${${PKG}_SOURCES_DIR})
@ -396,7 +489,7 @@ endforeach()
############################################
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
USER-QMMM)
if(ENABLE_${SIMPLE_LIB})
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
@ -417,40 +510,26 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
endif()
endforeach()
if(ENABLE_USER-AWPMD)
if(PKG_USER-AWPMD)
target_link_libraries(awpmd ${LAPACK_LIBRARIES})
endif()
if(ENABLE_USER-ATC)
if(PKG_USER-ATC)
target_link_libraries(atc ${LAPACK_LIBRARIES})
endif()
if(ENABLE_USER-H5MD)
if(PKG_USER-H5MD)
find_package(HDF5 REQUIRED)
target_link_libraries(h5md ${HDF5_LIBRARIES})
target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
endif()
if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
foreach(FSRC ${meam_SOURCES})
string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
if(FINDEX GREATER -1)
set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
endif()
endforeach()
endif()
if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
target_compile_options(reax PRIVATE -fno-second-underscore)
endif()
######################################################################
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
if(ENABLE_USER-OMP)
if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@ -467,7 +546,7 @@ if(ENABLE_USER-OMP)
include_directories(${USER-OMP_SOURCES_DIR})
endif()
if(ENABLE_KOKKOS)
if(PKG_KOKKOS)
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_definitions(-DLMP_KOKKOS)
@ -503,7 +582,7 @@ if(ENABLE_KOKKOS)
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
if(ENABLE_USER-DPD)
if(PKG_USER-DPD)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@ -516,7 +595,7 @@ if(ENABLE_KOKKOS)
include_directories(${KOKKOS_PKG_SOURCES_DIR})
endif()
if(ENABLE_OPT)
if(PKG_OPT)
set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
set(OPT_SOURCES)
set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
@ -530,7 +609,30 @@ if(ENABLE_OPT)
include_directories(${OPT_SOURCES_DIR})
endif()
if(ENABLE_USER-INTEL)
if(PKG_USER-INTEL)
if(NOT DEVELOPER_MODE)
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
endif()
option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON)
if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
endif()
include(CheckCXXCompilerFlag)
foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high)
check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}")
endif()
endforeach()
endif()
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@ -554,7 +656,7 @@ if(ENABLE_USER-INTEL)
include_directories(${USER-INTEL_SOURCES_DIR})
endif()
if(ENABLE_GPU)
if(PKG_GPU)
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h
@ -691,6 +793,7 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
# Actually add executable and lib to build
############################################
add_library(lammps ${LIB_SOURCES})
list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
@ -716,31 +819,60 @@ endif()
# Print package summary
##################################
foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
if(ENABLE_${PKG})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
endforeach()
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
include(FeatureSummary)
feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
message(STATUS "<<< Build configuration >>>
Build type ${CMAKE_BUILD_TYPE}
Install path ${CMAKE_INSTALL_PREFIX}
Compilers and Flags:
C++ Compiler ${CMAKE_CXX_COMPILER}
Type ${CMAKE_CXX_COMPILER_ID}
C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
Version ${CMAKE_CXX_COMPILER_VERSION}
C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines ${CPPFLAGS}")
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
if(LANGUAGES MATCHES ".*Fortran.*")
list (FIND LANGUAGES "Fortran" _index)
if (${_index} GREATER -1)
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
Type ${CMAKE_Fortran_COMPILER_ID}
Version ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
message(STATUS "Linker flags:
list (FIND LANGUAGES "C" _index)
if (${_index} GREATER -1)
message(STATUS "C Compiler ${CMAKE_C_COMPILER}
Type ${CMAKE_C_COMPILER_ID}
Version ${CMAKE_C_COMPILER_VERSION}
C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
endif()
if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Linker flags:
Executable ${CMAKE_EXE_LINKER_FLAGS}")
endif()
if(BUILD_SHARED_LIBS)
message(STATUS "Shared libries ${CMAKE_SHARED_LINKER_FLAGS}")
message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message(STATUS "Static libries ${CMAKE_STATIC_LINKER_FLAGS}")
message(STATUS "Static libraries ${CMAKE_STATIC_LINKER_FLAGS}")
endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
if(BUILD_MPI)
message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
endif()
if(ENABLED_GPU)
message(STATUS "GPU Api: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU Arch: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OpenCL")
message(STATUS "OCL Tune: ${OCL_TUNE}")
endif()
endif()
if(PKG_KSPACE)
message(STATUS "Using ${FFT} as FFT")
endif()

22
cmake/Modules/FindFFTW2.cmake
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@ -1,22 +0,0 @@
# - Find fftw2
# Find the native FFTW2 headers and libraries.
#
# FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
# FFTW2_LIBRARIES - List of libraries when using fftw2.
# FFTW2_FOUND - True if fftw2 found.
#
find_path(FFTW2_INCLUDE_DIR fftw.h)
find_library(FFTW2_LIBRARY NAMES fftw)
set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

25
cmake/Modules/FindFFTW3F.cmake Normal file
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@ -0,0 +1,25 @@
# - Find fftw3f
# Find the native FFTW3F headers and libraries.
#
# FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
# FFTW3F_LIBRARIES - List of libraries when using fftw3f.
# FFTW3F_FOUND - True if fftw3f found.
#
find_package(PkgConfig)
pkg_check_modules(PC_FFTW3F fftw3f)
find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )

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11
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@ -0,0 +1,11 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
\end{eqnarray*}
\end{document}

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Apr 2018 version">
<META NAME="docnumber" CONTENT="11 May 2018 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>
@ -19,7 +19,7 @@
:line
LAMMPS Documentation :c,h1
20 Apr 2018 version :c,h2
11 May 2018 version :c,h2
Version info: :h3

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4
doc/src/Section_commands.txt
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@ -684,6 +684,7 @@ package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
"bond/react"_fix_bond_react.html,
"colvars"_fix_colvars.html,
"dpd/energy (k)"_fix_dpd_energy.html,
"drude"_fix_drude.html,
@ -1211,7 +1212,8 @@ package"_Section_start.html#start_3.
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html :tb(c=4,ea=c)
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line

38
doc/src/Section_packages.txt
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@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
:line
USER-BOCS package :link(USER-BOCS),h4
[Contents:]
This package provides "fix bocs"_fix_bocs.html, a modified version
of "fix npt"_fix_nh.html which includes the pressure correction to
the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
[Install or un-install:]
make yes-user-bocs
make machine :pre
make no-user-bocs
make machine :pre
[Supporting info:]
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
See the following reference for information about the entire package:
Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
Example inputs are in the examples/USER/bocs folder.
:line
USER-CGDNA package :link(USER-CGDNA),h4
[Contents:]

11
doc/src/bond_oxdna.txt
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@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich2)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

21
doc/src/compute_ackland_atom.txt
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@ -10,19 +10,29 @@ compute ackland/atom command :h3
[Syntax:]
compute ID group-ID ackland/atom :pre
compute ID group-ID ackland/atom keyword/value :pre
ID, group-ID are documented in "compute"_compute.html command
ackland/atom = style name of this compute command :ul
ID, group-ID are documented in "compute"_compute.html command :ulb,l
ackland/atom = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {legacy} :l
{legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
:ule
[Examples:]
compute 1 all ackland/atom :pre
compute 1 all ackland/atom
compute 1 all ackland/atom legacy yes :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to the formulation given in "(Ackland)"_#Ackland.
Historically, LAMMPS had two, slightly different implementations of
the algorithm from the paper. With the {legacy} keyword, it is
possible to switch between the pre-2015 ({legacy yes}) and post-2015
implemention ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
@ -66,7 +76,8 @@ integers defined above.
"compute centro/atom"_compute_centro_atom.html
[Default:] none
[Default:]
The keyword {legacy} defaults to {no}.
:line

2
doc/src/compute_displace_atom.txt
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@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
displace/atom = style name of this compute command :l
zero or more keyword/arg pairs may be appended :l
keyword = {refresh} :
keyword = {refresh} :l
{replace} arg = name of per-atom variable :pre
:ule

21
doc/src/compute_sna_atom.txt
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@ -161,9 +161,9 @@ function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
the calculated bispectrum components. This optional keyword is only
available for compute {sna/atom}, as {snad/atom} and {snav/atom}
are unaffected by the removal of constant terms.
the calculated bispectrum components. This optional keyword
normally only affects compute {sna/atom}. However, when
{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.
The keyword {quadraticflag} determines whether or not the
quadratic analogs to the bispectrum quantities are generated.
@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
If the {quadratic} keyword value is set to 1, then additional
columns are appended to each per-atom array, corresponding to
columns are generated, corresponding to
the products of all distinct pairs of bispectrum components. If the
number of bispectrum components is {K}, then the number of distinct pairs
is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same
ordering of sub-blocks as was used for the bispectrum
components. Within each sub-block, the ordering is upper-triangular,
(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
is {K}({K}+1)/2.
For compute {sna/atom} these columns are appended to existing {K} columns.
The ordering of quadratic terms is upper-triangular,
(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}).
For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2
additional columns is inserted directly after each of sub-block
of linear terms i.e. linear and quadratic terms are contiguous.
So the nesting order from inside to outside is bispectrum component,
linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
from a compute as input. See "Section

205
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@ -0,0 +1,205 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style table/cut command :h3
[Syntax:]
dihedral_style table/cut style Ntable :pre
style = {linear} or {spline} = method of interpolation
Ntable = size of the internal lookup table :ul
[Examples:]
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre
[Description:]
The {table/cut} dihedral style creates interpolation tables of length
{Ntable} from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". In addition, an
analytic cutoff that is quadratic in the bond-angle (theta) is applied
in order to regularize the dihedral interaction. The dihedral table
files are read by the "dihedral_coeff"_dihedral_coeff.html command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
{Ntable} dihedral angles. During a simulation, these tables are used
to interpolate energy and force values on individual atoms as
needed. The interpolation is done in one of 2 styles: {linear} or
{spline}.
For the {linear} style, the dihedral angle (phi) is used to find 2
surrounding table values from which an energy or its derivative is
computed by linear interpolation.
For the {spline} style, cubic spline coefficients are computed and
stored at each of the {Ntable} evenly-spaced values in the
interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the "dihedral_coeff"_dihedral_coeff.html command as in the example
above.
style (aat)
cutoff prefactor
cutoff angle1
cutoff angle2
filename
keyword :ul
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
:c,image(Eqs/dihedral_table_cut.jpg)
The cutoff specifies an prefactor to the cutoff function. While this value
would ordinarily equal 1 there may be situations where the value should change.
The cutoff angle1 specifies the angle (in degrees) below which the dihedral
interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between angle1 and angle2, which is the angle at
which the cutoff function drops to zero. The value of zero effectively "turns
off" the dihedral interaction.
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
:line
The format of a tabulated file is as follows (without the
parenthesized comments). It can begin with one or more comment
or blank lines.
# Table of the potential and its negative derivative :pre
DIH_TABLE1 (keyword is the first text on line)
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
(blank line)
1 -168.0 -1.40351172223 0.0423346818422
2 -156.0 -1.70447981034 0.00811786522531
3 -144.0 -1.62956100432 -0.0184129719987
...
30 180.0 -0.707106781187 0.0719306095245 :pre
# Example 2: table of the potential. Forces omitted :pre
DIH_TABLE2
N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
1 -168.0 -1.40351172223
2 -156.0 -1.70447981034
3 -144.0 -1.62956100432
...
30 180.0 -0.707106781187 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in
any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value, the 3rd value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the
energy of the 4-atom configuration for the specified angle. The 4th
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
are still energy, not force. The dihedral angle values must increase
from one line to the next.
Dihedral table splines are cyclic. There is no discontinuity at 180
degrees (or at any other angle). Although in the examples above, the
angles range from -180 to 180 degrees, in general, the first angle in
the list can have any value (positive, zero, or negative). However
the {range} of angles represented in the table must be {strictly} less
than 360 degrees (2pi radians) to avoid angle overlap. (You may not
supply entries in the table for both 180 and -180, for example.) If
the user's table covers only a narrow range of dihedral angles,
strange numerical behavior can occur in the large remaining gap.
[Parameters:]
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the N
specified in the "dihedral_style table"_dihedral_style.html command.
Let {Ntable} is the number of table entries requested dihedral_style
command, and let {Nfile} be the parameter following "N" in the
tabulated file ("30" in the sparse example above). What LAMMPS does
is a preliminary interpolation by creating splines using the {Nfile}
tabulated values as nodal points. It uses these to interpolate as
needed to generate energy and derivative values at {Ntable} different
points (which are evenly spaced over a 360 degree range, even if the
angles in the file are not). The resulting tables of length {Ntable}
are then used as described above, when computing energy and force for
individual dihedral angles and their atoms. This means that if you
want the interpolation tables of length {Ntable} to match exactly what
is in the tabulated file (with effectively nopreliminary
interpolation), you should set {Ntable} = {Nfile}. To insure the
nodal points in the user's file are aligned with the interpolated
table entries, the angles in the table should be integer multiples of
360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the the {Ntable} different entries in the
interpolated energy table to a file to make sure that the interpolated
function agrees with the user's expectations. (Note: You can
temporarily increase the {Ntable} parameter to a high value for this
purpose. "{Ntable}" is explained above.)
The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
It is followed by a filename, and it allows the user to check the
interpolated force table. This option is available even if the user
selected the "NOF" option.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html
[Default:] none
:link(dihedralcut-Salerno)
[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

1
doc/src/dihedrals.txt
View File

@ -19,6 +19,7 @@ Dihedral Styles :h1
dihedral_quadratic
dihedral_spherical
dihedral_table
dihedral_table_cut
dihedral_zero
dihedral_charmm
dihedral_class2

19
doc/src/dump_modify.txt
View File

@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
these keywords apply to various dump styles :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
{image} arg = {yes} or {no}
{label} arg = string
string = character string (e.g. BONDS) to use in header of dump local file
{maxfiles} arg = Fmax
Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
{nfile} arg = Nf
Nf = write this many files, one from each of Nf processors
{pad} arg = Nchar = # of characters to convert timestep to
@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
:line
The {maxfiles} keyword can only be used when a '*' wildcard is
included in the dump file name, i.e. when writing a new file(s) for
each snapshot. The specified {Fmax} is how many snapshots will be
kept. Once this number is reached, the file(s) containing the oldest
snapshot is deleted before a new dump file is written. If the
specified {Fmax} <= 0, then all files are retained.
This can be useful for debugging, especially if you don't know on what
timestep something bad will happen, e.g. when LAMMPS will exit with an
error. You can dump every timestep, and limit the number of dump
files produced, even if you run for 1000s of steps.
:line
The {nfile} or {fileper} keywords can be used in conjunction with the
"%" wildcard character in the specified dump file name, for all dump
styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@ -901,6 +917,7 @@ flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
maxifiles = -1
nfile = 1
pad = 0
pbc = no

112
doc/src/fix_bocs.txt Normal file
View File

@ -0,0 +1,112 @@
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bocs command :h3
[Syntax:]
fix ID group-ID bocs keyword values ... :pre
keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
{temp} values = Tstart Tstop Tdamp
{cgiso} values = Pstart Pstop Pdamp
{basis set}
{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
{linear_spline} values = input_filename
{cubic_spline} values = input_filename :pre
:ule
[Examples:]
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
thermo_modify press 1_press :pre
[Description:]
These commands incorporate a pressure correction as described by
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
The first half of the command mimics a standard fix npt command:
fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
The two differences are replacing {npt} with {bocs}, and replacing
{iso}/{aniso}/{etc} with {cgiso}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:
Volume_i, PressureCorrection_i :pre
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
With the {analytic} option, the arguments are as follows:
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.
[Restrictions:]
As this is computing a (modified) pressure, group-ID should be {all}.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
By default, LAMMPS will still report the normal value for the pressure
if the pressure is printed via a {thermo} command, or if the pressures
are written to a file every so often. In order to have LAMMPS report the
modified pressure, you must include the {thermo_modify} command given in
the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
This fix is part of the USER-BOCS package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related:]
For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on github"_bocsgithub and read the release
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
:link(bocsgithub,https://github.com/noid-group/BOCS)
:line
:link(bocs-Dunn1)
[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
:link(bocs-Martyna)
[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
:link(bocs-Dunn2)
[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).

332
doc/src/fix_bond_react.txt Normal file
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@ -0,0 +1,332 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bond/react command :h3
[Syntax:]
fix ID group-ID bond/react common_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
... :pre
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
bond/react = style name of this fix command :l
zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
these apply to all reaction specifications (below) :l
common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization
{yes} = perform reaction site stabilization
{group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
{xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
react = mandatory argument indicating new reaction specification :l
react-ID = user-assigned name for the reaction :l
react-group-ID = only atoms in this group are available for the reaction :l
Nevery = attempt reaction every this many steps :l
Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l
individual_keyword = {prob} or {stabilize_steps} :l
{prob} values = fraction seed
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
{stabilize_steps} value = timesteps
timesteps = number of timesteps to apply internally created nve/limit.html :pre
:ule
[Examples:]
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
molecule mol1 pre_reacted_rxn1.txt
molecule mol2 post_reacted_rxn1.txt
molecule mol3 pre_reacted_rxn2.txt
molecule mol4 post_reacted_rxn2.txt
fix 5 all bond/react stabilization yes nvt_grp .03 &
react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
[Description:]
Initiate complex covalent bonding (topology) changes. These topology
changes will be referred to as 'reactions' throughout this
documentation. Topology changes are defined in pre- and post-reaction
molecule templates and can include creation and deletion of bonds,
angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
atom-types, or atomic charges.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
determine bonding changes a priori. Rather, it uses a distance-based
probabilistic criteria to effect predetermined topology changes in
simulations using standard force fields.
This fix was created to facilitate the dynamic creation of polymeric,
amorphous or highly-crosslinked systems. A suggested workflow for
using this fix is: 1) identify a reaction to be simulated 2) build a
molecule template of the reaction site before the reaction has
occurred 3) build a molecule template of the reaction site after the
reaction has occurred 4) create a map that relates the
template-atom-IDs of each atom between pre- and post-reaction molecule
templates 5) fill a simulation box with molecules and run a simulation
with fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple {react}
arguments to a single 'fix bond/react' command. This syntax is
necessary because the 'common keywords' are applied to all reactions.
The {stabilization} keyword enables reaction site stabilization.
Reaction site stabilization is performed by including reacting atoms
in an internally created fix "nve/limit"_fix_nve_limit.html time
integrator for a set number of timesteps given by the
{stabilize_steps} keyword. While reacting atoms are being time
integrated by the internal nve/limit, they are prevented from being
involved in any new reactions. The {xmax} value keyword should
typically be set to the maximum distance that non-reacting atoms move
during the simulation.
The group-ID set using the {stabilization} keyword should be a
previously unused group-ID. It cannot be specified as 'all'. The fix
bond/react command creates a "dynamic group"_group.html of this name
that includes all non-reacting atoms. This dynamic group-ID should
then be used by a subsequent system-wide time integrator such as nvt,
npt, or nve, as shown in the second example above. It is currently
necessary to place the time integration command after the fix
bond/react command due to the internal dynamic grouping performed by
fix bond/react.
NOTE: The internally created group currently applies to all atoms in
the system, i.e. you should generally not have a separate thermostat
which acts on the 'all' group.
The following comments pertain to each {react} argument:
A check for possible new reaction sites is performed every {Nevery}
timesteps.
Two conditions must be met for a reaction to occur. First a bonding
atom pair must be identified. Second, the topology surrounding the
bonding atom pair must match the topology of the pre-reaction
template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms within the specified react-group-ID of type
typei and typej must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
chosen. Then, if both an atomi and atomj have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
reactions that involve a given atom on the same timestep. If this is
the case, only one such reaction is permitted to occur. This reaction
is chosen randomly from all potential reactions. This capability
allows e.g. for different reaction pathways to proceed from identical
reaction sites with user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
surrounding topology. As described below, the bonding atom pairs of
the pre-reacted template are specified by atom ID in the map file. The
pre-reacted molecule template should contain as few atoms as possible
while still completely describing the topology of all atoms affected
by the reaction. For example, if the force field contains dihedrals,
the pre-reacted template should contain any atom within three bonds of
reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the
rest of a long polymer chain. These are referred to as edge atoms, and
are also specified in the map file.
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template
must be the same as those of a potential reaction site in the
simulation. A detailed discussion of matching molecule template atom
types with the simulation is provided on the "molecule"_molecule.html
command page.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It
must contain the same number of atoms as the pre-reacted template. A
one-to-one correspondence between the atom IDs in the pre- and
post-reacted templates is specified in the map file as described
below. Note that during a reaction, an atom, bond, etc. type may
change to one that was previously not present in the simulation. These
new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
"molecule"_molecule.html command page.
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and one optional keyword. The mandatory
keyword is 'equivalences' and the optional keyword is 'edgeIDs':
N {equivalences} = # of atoms N in the reaction molecule templates
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
The body of the map file contains two mandatory sections and one
optional section. The first mandatory section begins with the keyword
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
pre-reacted molecule template. The second mandatory section begins
with the keyword 'Equivalences' and lists a one-to-one correspondence
between atom IDs of the pre- and post-reacted templates. The first
column is an atom ID of the pre-reacted molecule template, and the
second column is the corresponding atom ID of the post-reacted
molecule template. The optional section begins with the keyword
'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
molecule template.
A sample map file is given below:
:line
# this is a map file :pre
2 edgeIDs
7 equivalences :pre
BondingIDs :pre
3
5 :pre
EdgeIDs :pre
1
7 :pre
Equivalences :pre
1 1
2 2
3 3
4 4
5 5
6 6
7 7 :pre
:line
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
angles, dihedrals or impropers are supported.
A few capabilities to note: 1) You may specify as many {react}
arguments as desired. For example, you could break down a complicated
reaction mechanism into several reaction steps, each defined by its
own {react} argument. 2) While typically a bond is formed or removed
between the bonding atom pairs specified in the pre-reacted molecule
template, this is not required. 3) By reversing the order of the pre-
and post- reacted molecule templates in another {react} argument, you
can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
it occurs.
The {prob} keyword can affect whether an eligible reaction actually
occurs. The fraction setting must be a value between 0.0 and 1.0. A
uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction.
The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
overall system thermostat.
In order to produce the most physical behavior, this 'reaction site
equilibration time' should be tuned to be as small as possible while
retaining stability for a given system or reaction step. After a
limited number of case studies, this number has been set to a default
of 60 timesteps. Ideally, it should be individually tuned for each fix
reaction step. Note that in some situations, decreasing rather than
increasing this parameter will result in an increase in stability.
A few other considerations:
It may be beneficial to ensure reacting atoms are at a certain
temperature before being released to the overall thermostat. For this,
you can use the internally-created dynamic group named
"bond_react_MASTER_group." For example, adding the following command
would thermostat the group of all atoms currently involved in a
reaction:
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
NOTE: This command must be added after the fix bond/react command, and
will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
neighbor lists (for bond-forming reactions) and computes distances
between pairs of atoms in the list. It also communicates between
neighboring processors to coordinate which bonds are created and/or
removed. All of these operations increase the cost of a timestep. Thus
you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the dump
local command.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html, aside from internally-created per-atom
properties. None of the "fix_modify"_fix_modify.html options are
relevant to this fix.
This fix computes one statistic for each {react} argument that it
stores in a global vector, of length 'number of react arguments', that
can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated by
this fix are "intensive".
These is 1 quantity for each react argument:
(1) cumulative # of reactions occurred :ul
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.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix
bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
"dump local"_dump.html, "special_bonds"_special_bonds.html
[Default:]
The option defaults are stabilization = no, stabilize_steps = 60
:line
:link(Gissinger)
[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).

2
doc/src/fix_langevin_drude.txt
View File

@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the
self-consistent minimization. It must however be high enough, so that
the dipoles can follow the local electric field exerted by the
neighbouring atoms. The optimal value probably depends on the
neighboring atoms. The optimal value probably depends on the
temperature of the centers of mass and on the mass of the Drude
particles.

36
doc/src/fix_modify.txt
View File

@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre
fix-ID = ID of the fix to modify :ulb,l
one or more keyword/value pairs may be appended :l
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{energy} value = {yes} or {no}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
{bodyforces} value = {early} or {late}
early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
[Examples:]
@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the
relaxation criteria, although this seems unlikely.
NOTE: This option is only supported by fixes that explicitly say
so. For some of these (e.g. the
"fix shake"_fix_shake.html command) the default setting is
{virial yes}, for others it is {virial no}.
so. For some of these (e.g. the "fix shake"_fix_shake.html command)
the default setting is {virial yes}, for others it is {virial no}.
For fixes that set or modify forces, it may be possible to select at
which "r-RESPA"_run_style.html level the fix operates via the {respa}
@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify
dynamic/dof"_compute_modify.html command for a similar way to insure
correct temperature normalization for those thermostats.
The {bodyforces} keyword determines whether the forces and torques
acting on rigid bodies are computed {early} at the post-force stage of
each timestep (right after per-atom forces have been computed and
communicated among processors), or {late} at the final-integrate stage
of each timestep (after any other fixes have finished their post-force
tasks). Only the rigid-body integration fixes use this option, which
includes "fix rigid"_fix_rigid.html and "fix
rigid/small"_fix_rigid.html, and their variants, and also "fix
poems"_fix_poems.html.
The default is {late}. If there are other fixes that add forces to
individual atoms, then the rigid-body constraints will include these
forces when time-integrating the rigid bodies. If {early} is
specified, then new fixes can be written that use or modify the
per-body force and torque, before time-integration of the rigid bodies
occurs. Note however this has the side effect, that fixes such as
"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
"fix spring"_fix_spring.html, which add forces to individual atoms
will have no effect on the motion of the rigid bodies if they are
specified in the input script after the fix rigid command. LAMMPS
will give a warning if that is the case.
[Restrictions:] none
[Related commands:]
@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
[Default:]
The option defaults are temp = ID defined by fix, press = ID defined
by fix, energy = no, virial = different for each fix style, respa = 0.
by fix, energy = no, virial = different for each fix style, respa = 0,
bodyforce = late.

18
doc/src/fix_poems.txt
View File

@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. 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 access by various "output
commands"_Section_howto.html#howto_15. 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.
files"_restart.html.
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
this fix style to set whether per-body forces and torques are computed
early or late in a timestep, i.e. at the post-force stage or at the
final-integrate stage, respectively.
No global or per-atom quantities are stored by this fix for access by
various "output commands"_Section_howto.html#howto_15. 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.
[Restrictions:]

2
doc/src/fix_reax_bonds.txt
View File

@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
The specified group-ID is ignored by this fix.
The format of the output file should be reasonably self-explanatory.
The meaning of the column header abbreviations is as follows:

29
doc/src/fix_restrain.txt
View File

@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi0 = equilibrium dihedral angle phi (degrees) :pre
phi0 = equilibrium dihedral angle phi (degrees)
keyword/value = optional keyword value pairs. supported keyword/value pairs:
{mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
:ule
[Examples:]
@ -155,11 +157,13 @@ associated with the restraint is
with the following coefficients:
K (energy)
n = 1
n (multiplicity, >= 0)
d (degrees) = phi0 + 180 :ul
K and phi0 are specified with the fix. Note that the value of n is
hard-wired to 1. Also note that the energy will be a minimum when the
K and phi0 are specified with the fix. Note that the value of the
dihedral multiplicity {n} is set by default to 1. You can use the
optional {mult} keyword to set it to a different positive integer.
Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.
:line
@ -183,10 +187,17 @@ added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
This fix computes a global scalar, which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
potential energy for all the restraints as discussed above. The scalar
value calculated by this fix is "extensive".
This fix computes a global scalar and a global vector of length 3, which
can be accessed by various "output commands"_Section_howto.html#howto_15.
The scalar is the total potential energy for {all} the restraints as
discussed above. The vector values are the sum of contributions to the
following individual categories:
1 = bond energy
2 = angle energy
3 = dihedral energy :ul
The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.

13
doc/src/fix_rigid.txt
View File

@ -223,10 +223,10 @@ via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule} or {custom}, you can define a system that has
no rigid bodies initially. This is useful when you are using the {mol}
keyword in conjunction with another fix that is adding rigid bodies
on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
"fix pour"_fix_pour.html.
no rigid bodies initially. This is useful when you are using the
{mol} keyword in conjunction with another fix that is adding rigid
bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
or "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@ -742,6 +742,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2
NVT rigid fixes do not use any external compute to compute
instantaneous temperature.
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
all rigid styles to set whether per-body forces and torques are
computed early or late in a timestep, i.e. at the post-force stage or
at the final-integrate stage or the timestep, respectively.
The 2 NVE rigid fixes compute a global scalar which can be accessed by
various "output commands"_Section_howto.html#howto_15. The scalar
value calculated by these fixes is "intensive". The scalar is the

2
doc/src/fixes.txt
View File

@ -20,9 +20,11 @@ Fixes :h1
fix_ave_time
fix_aveforce
fix_balance
fix_bocs
fix_bond_break
fix_bond_create
fix_bond_swap
fix_bond_react
fix_box_relax
fix_cmap
fix_colvars

3
doc/src/lammps.book
View File

@ -135,8 +135,10 @@ fix_ave_histo.html
fix_ave_time.html
fix_aveforce.html
fix_balance.html
fix_bocs.html
fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
fix_cmap.html
@ -580,6 +582,7 @@ dihedral_opls.html
dihedral_quadratic.html
dihedral_spherical.html
dihedral_table.html
dihedral_table_cut.html
dihedral_zero.html
lammps_commands_improper.html

2
doc/src/pair_kolmogorov_crespi_z.txt
View File

@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above.
This potential is intended for interactions between two layers of graphene.
Therefore, to avoid interaction between layers in multi-layered materials,
each layer should have a separate atom type and interactions should only
be computed between atom types of neighbouring layers.
be computed between atom types of neighboring layers.
The parameter file (e.g. CC.KC), is intended for use with metal
"units"_units.html, with energies in meV. An additional parameter, {S},

11
doc/src/pair_oxdna.txt
View File

@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich1)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc1)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

11
doc/src/pair_oxdna2.txt
View File

@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc2)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

6
examples/USER/bocs/README Normal file
View File

@ -0,0 +1,6 @@
This folder contains the files to run a NPT simulation of 1 site CG methanol
while employing a correction to the barostat.
The pair force was computed via the Multi-Scale Coarse-Graining method.
The resulting model was then iteratively pressure matched.
The model accurately reproduces both structural (RDF) and thermodynamic
(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.

69
examples/USER/bocs/in.methanol Normal file
View File

@ -0,0 +1,69 @@
units real
dimension 3
boundary p p p
atom_style atomic
newton on
timestep 1.0
read_data methanol.data
velocity all create 300.0 16802 dist gaussian
pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
thermo 500
thermo_style custom step temp pe etotal press vol
variable STEP equal step
variable TEMP equal temp
## volume from cubic angstroms to cubic nm
variable VOL equal vol/1000.0
## pressure from atm to bar
variable PRESS equal press*1.01325
variable PXX equal pxx*1.01325
variable PYY equal pyy*1.01325
variable PZZ equal pzz*1.01325
variable PXY equal pxy*1.01325
variable PXZ equal pxz*1.01325
variable PYZ equal pyz*1.01325
## energy from kcal/mol to kJ/mol
variable KE equal ke*4.184
variable PE equal pe*4.184
variable UVDW equal evdwl*4.184
##### SPECIAL COMMANDS FOR FIX_BOCS #####
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
# Report the modified pressure
thermo_modify press 1_press
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet
run 10000

2505
examples/USER/bocs/lammps_nb_MET-MET.table Normal file
View File

File diff suppressed because it is too large Load Diff

143
examples/USER/bocs/log.20Apr18.methanol.g++.1 Normal file
View File

@ -0,0 +1,143 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
boundary p p p
atom_style atomic
newton on
timestep 1.0
read_data methanol.data
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
1 by 1 by 1 MPI processor grid
reading atoms ...
968 atoms
velocity all create 300.0 16802 dist gaussian
pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
thermo 500
thermo_style custom step temp pe etotal press vol
variable STEP equal step
variable TEMP equal temp
## volume from cubic angstroms to cubic nm
variable VOL equal vol/1000.0
## pressure from atm to bar
variable PRESS equal press*1.01325
variable PXX equal pxx*1.01325
variable PYY equal pyy*1.01325
variable PZZ equal pzz*1.01325
variable PXY equal pxy*1.01325
variable PXZ equal pxz*1.01325
variable PYZ equal pyz*1.01325
## energy from kcal/mol to kJ/mol
variable KE equal ke*4.184
variable PE equal pe*4.184
variable UVDW equal evdwl*4.184
##### SPECIAL COMMANDS FOR FIX_BOCS #####
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
# Report the modified pressure
thermo_modify press 1_press
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 24
ghost atom cutoff = 24
binsize = 12, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 4.691 | 4.691 | 4.691 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 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 | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
Other | | 0.1252 | | | 0.36
Nlocal: 968 ave 968 max 968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9112 ave 9112 max 9112 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 404392 ave 404392 max 404392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 404392
Ave neighs/atom = 417.76
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34

143
examples/USER/bocs/log.20Apr18.methanol.g++.4 Normal file
View File

@ -0,0 +1,143 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
boundary p p p
atom_style atomic
newton on
timestep 1.0
read_data methanol.data
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
1 by 2 by 2 MPI processor grid
reading atoms ...
968 atoms
velocity all create 300.0 16802 dist gaussian
pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
thermo 500
thermo_style custom step temp pe etotal press vol
variable STEP equal step
variable TEMP equal temp
## volume from cubic angstroms to cubic nm
variable VOL equal vol/1000.0
## pressure from atm to bar
variable PRESS equal press*1.01325
variable PXX equal pxx*1.01325
variable PYY equal pyy*1.01325
variable PZZ equal pzz*1.01325
variable PXY equal pxy*1.01325
variable PXZ equal pxz*1.01325
variable PYZ equal pyz*1.01325
## energy from kcal/mol to kJ/mol
variable KE equal ke*4.184
variable PE equal pe*4.184
variable UVDW equal evdwl*4.184
##### SPECIAL COMMANDS FOR FIX_BOCS #####
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
# Report the modified pressure
thermo_modify press 1_press
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 24
ghost atom cutoff = 24
binsize = 12, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 3.37 | 3.37 | 3.371 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
Other | | 0.3112 | | | 1.08
Nlocal: 242 ave 244 max 239 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5718.5 ave 5736 max 5702 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 100703 ave 108064 max 93454 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 402813
Ave neighs/atom = 416.129
Neighbor list builds = 14
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:28

991
examples/USER/bocs/methanol.data Normal file
View File

@ -0,0 +1,991 @@
LAMMPS Description
968 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
0 bond types
0 angle types
0 dihedral types
0 40.4635 xlo xhi
0 40.4635 ylo yhi
0 40.4635 zlo zhi
Masses
1 32.0424
Atoms
1 1 36.39 8.05 27.55
2 1 18.38 15.72 26.03
3 1 3.52 1.77 23.57
4 1 31.09 11.38 12.17
5 1 13.3 34.8 2.89
6 1 1.72 38.55 10.36
7 1 38.6 23.16 6.19
8 1 0.74 33.21 0.17
9 1 26.97 9.53 11.24
10 1 31.68 12.19 17.04
11 1 15.19 9.06 0.2
12 1 34.39 20.63 35.71
13 1 21.79 4.93 6.49
14 1 28.08 33.01 24.51
15 1 37.03 20.52 32.9
16 1 32.69 20 30.11
17 1 23.77 38.59 18.79
18 1 16.01 2.31 20.15
19 1 5.65 15.5 28.5
20 1 8.35 17.35 20.48
21 1 31.24 24.68 27.4
22 1 29.41 16.64 19.79
23 1 37.42 31.93 26.68
24 1 18.76 39.06 30.68
25 1 22.97 35 20.81
26 1 39.47 18.28 29.6
27 1 34.37 19.4 0.17
28 1 5.94 9.53 10.95
29 1 11.45 38.44 14.64
30 1 39.57 11.04 1.57
31 1 25.91 20.97 12.79
32 1 36.3 22.1 1.68
33 1 21.87 22.49 3.43
34 1 5.77 18.66 3.97
35 1 7 7.59 18.42
36 1 39.76 27.63 17.98
37 1 10.26 23.18 5.11
38 1 23.23 21.37 17.38
39 1 7.47 37.37 5.57
40 1 0.73 21.6 14.78
41 1 2.27 30.22 14.93
42 1 7.39 28.22 14.88
43 1 27.48 1.11 25.02
44 1 8.37 13.19 14.64
45 1 7.11 33.57 0.65
46 1 34.19 35.11 3.17
47 1 7.52 3.2 20.33
48 1 1.02 17.69 37.85
49 1 8.59 6.21 10.26
50 1 2.89 16.81 30.02
51 1 27.05 9.07 32.8
52 1 12.32 14.79 21.11
53 1 26.63 22.69 16.75
54 1 31.6 2.79 20.45
55 1 35.11 0.74 12.16
56 1 29.71 31.23 37.63
57 1 38.22 19.02 18.12
58 1 10.95 17.4 0.39
59 1 1.65 19.87 6.67
60 1 5.15 1.94 14.61
61 1 8.2 31.43 15.72
62 1 0.55 20.85 2.45
63 1 15.27 31.74 0.33
64 1 17.9 9.84 23.87
65 1 1.46 8.39 19.24
66 1 37.79 25.11 12.24
67 1 14.11 27.19 30.7
68 1 29.39 24.12 38.92
69 1 39.15 20.32 39.86
70 1 11.79 11.38 30.6
71 1 29.87 30.18 32.5
72 1 11.06 37.8 30.18
73 1 20.11 4.59 35.57
74 1 37.19 27.23 1.44
75 1 18.83 26.13 35.26
76 1 29.27 7.86 36.75
77 1 34.83 29.59 37.82
78 1 22.16 34.68 25.27
79 1 5.95 14.65 25.55
80 1 -0.04 3.48 29.91
81 1 14.69 6.75 38.06
82 1 16.8 23.69 3.14
83 1 14.52 38.72 21.61
84 1 37.36 15.13 27.98
85 1 29.79 17.03 27.55
86 1 21.01 0.39 0.9
87 1 35.3 6.45 14.41
88 1 13.74 34.69 10.01
89 1 13.83 7.92 31.88
90 1 26.88 37.81 22.36
91 1 31.76 7.34 10.03
92 1 11.98 37.49 19.61
93 1 29.19 31.74 20.69
94 1 39.15 10.97 21.06
95 1 1.47 5 22.21
96 1 -0.1 1.33 16.26
97 1 34.74 34.78 30.66
98 1 22.09 26.78 2.27
99 1 36.58 34.8 16.19
100 1 19.09 24.88 15.75
101 1 2.21 31.42 38.32
102 1 28.02 8.18 29.77
103 1 15.99 16.78 17.61
104 1 32.43 12.2 35.3
105 1 26.54 38.8 30.88
106 1 35.58 22.23 18.31
107 1 28.3 30.81 2.96
108 1 8.95 32.9 9.02
109 1 28.51 30.02 29.39
110 1 13 5.35 34.26
111 1 37.9 36.79 1.37
112 1 12.78 1.99 40.66
113 1 21.19 34.55 17.45
114 1 10.5 20 5.07
115 1 16.19 21.64 18.49
116 1 14.62 26.41 19.88
117 1 27.97 2.89 28.03
118 1 29.44 14.35 39.04
119 1 2.29 24.16 33.8
120 1 39.22 15.81 32.02
121 1 7.31 19.66 18.18
122 1 27.67 7.98 15.53
123 1 31.23 4.04 33
124 1 29.52 39.44 28.71
125 1 30.86 20.28 15.84
126 1 32.25 7.44 19.79
127 1 34.68 15.68 1.18
128 1 16.58 27.98 27.97
129 1 32.27 24.24 15.82
130 1 3.86 6.57 39.8
131 1 9.1 2.88 13.12
132 1 17.84 27.8 11.79
133 1 4.77 10.88 6.75
134 1 16.58 24.21 24.5
135 1 10.17 19.31 38.32
136 1 6.27 7.81 36.44
137 1 34.76 37.89 29.76
138 1 40.99 38.22 35.21
139 1 25.04 21.79 36.88
140 1 4.78 15.35 16.44
141 1 19.24 5.77 40.18
142 1 13.59 11.27 37.14
143 1 1.61 23.83 39.61
144 1 6.02 33.07 3.77
145 1 0.85 7.4 35.42
146 1 6.47 40.34 4.65
147 1 16.45 36.52 15.44
148 1 19.58 9.5 1.64
149 1 1.36 1.72 35.53
150 1 11.74 5.48 4.98
151 1 25.45 40.36 15.44
152 1 19.09 0.74 36.18
153 1 31.78 37.98 1.84
154 1 23.26 18.47 38.56
155 1 7.29 22.87 25.86
156 1 2.36 7.83 8.78
157 1 39.61 25.94 21.12
158 1 7.78 18.97 25.29
159 1 36.56 19.61 26.7
160 1 4.64 12.06 19.9
161 1 21.05 33.08 0.87
162 1 33.93 22.87 39.71
163 1 33.62 29.48 20.83
164 1 0.64 18.79 9.52
165 1 27.53 16.7 22.51
166 1 17.66 9.84 14.61
167 1 31.23 22.44 24.98
168 1 39.3 34.88 11.03
169 1 24.01 10.56 0.09
170 1 15.81 33.44 18.52
171 1 19.92 30.61 19.25
172 1 16.49 3.95 38.28
173 1 18.6 38.87 24.98
174 1 33.04 25.55 8.57
175 1 16.9 35.09 22.94
176 1 15.18 6.74 2.33
177 1 40.54 12.58 31.65
178 1 21.21 37.62 14.35
179 1 33.52 38.19 14.89
180 1 22.06 12.49 29.81
181 1 19.49 29.03 2.52
182 1 26.97 18.55 38.45
183 1 24.1 11.86 17.22
184 1 12.02 0.55 10.39
185 1 3.8 35.94 19.94
186 1 8.31 14.31 37.4
187 1 29.03 8.28 22.92
188 1 18.92 0.22 27.87
189 1 26.79 24.9 24.62
190 1 36.59 18.86 21.13
191 1 33.06 13.58 30.17
192 1 32.37 2.02 39.69
193 1 22.65 25.97 32.59
194 1 21.81 38.04 33.85
195 1 36.82 37.68 19.22
196 1 32.48 31.43 33.66
197 1 8.75 36.66 20.34
198 1 14.88 15.11 28.76
199 1 22.83 28.55 29.5
200 1 2.98 12.06 2.88
201 1 3.01 37 6.91
202 1 14.79 16.69 3.66
203 1 12.62 38.28 0.97
204 1 40.07 21.27 25.25
205 1 34.58 6.14 39.48
206 1 11.51 30.52 33.53
207 1 32.22 9.28 30.52
208 1 0.7 4.01 38.87
209 1 32.66 39.86 36.84
210 1 27.34 34.57 21.76
211 1 13.7 23.12 8.34
212 1 28 9.71 6.29
213 1 31.69 26.39 38.19
214 1 2.04 20.93 36.95
215 1 30.31 26.61 12.31
216 1 25.37 20.63 9.4
217 1 16.29 5.62 14.04
218 1 1.36 1.95 4.97
219 1 38.75 26.8 5.62
220 1 40.28 29.89 12.27
221 1 0.52 31.22 7.58
222 1 15.64 21.64 14.71
223 1 10.11 28.8 9.67
224 1 19.03 37.3 38.87
225 1 12.07 6.46 19.25
226 1 36.22 21.11 15.02
227 1 12.49 15.69 7.21
228 1 25.2 30.8 19.71
229 1 8.24 35.22 23.02
230 1 9.94 4.1 1.86
231 1 4.31 19.07 26.23
232 1 22.03 19.99 14.19
233 1 30.84 5.24 2.75
234 1 35.51 30.52 32.3
235 1 3.88 20.41 39.48
236 1 30.86 0.39 31.56
237 1 25.91 27.12 39.04
238 1 33.39 5.37 4.51
239 1 20.58 28.33 37.53
240 1 11.83 21.81 39.11
241 1 39.94 5.2 5.73
242 1 29.89 33.21 15.44
243 1 23.42 15.38 30.98
244 1 28.66 11.56 16.13
245 1 16.74 20.43 21.72
246 1 9.31 0.26 22.42
247 1 4.38 37.78 14.12
248 1 13.86 4.65 16.99
249 1 6.72 27.43 8.14
250 1 33.45 18.74 19.98
251 1 17.34 14.55 35.57
252 1 14.21 37.39 28.76
253 1 26.29 29.06 22.26
254 1 36.52 26.18 15.62
255 1 17.6 8.81 10.14
256 1 21.95 25.19 17.69
257 1 17.4 7.46 18.59
258 1 6.15 29.7 35.99
259 1 9.73 37.39 24.96
260 1 28.58 28.21 36.19
261 1 8.24 13.72 32.2
262 1 13.25 34.6 22.71
263 1 38.58 7.98 10.3
264 1 18.29 29.75 23.51
265 1 3.74 13.22 31.05
266 1 30.78 0.7 24.57
267 1 24.5 12.94 10.81
268 1 33.88 26.44 1.96
269 1 29.92 22.6 9.59
270 1 15.87 21.94 33.44
271 1 23.63 8.41 10.95
272 1 26.53 0.01 7.58
273 1 33.88 8.73 2.52
274 1 39.74 31.46 36.87
275 1 13.28 39.54 37
276 1 24.74 35.41 32.14
277 1 17.3 34.32 6.85
278 1 24.43 13.36 5.63
279 1 31.23 17.12 7.11
280 1 15.58 37.85 34.06
281 1 25.93 38.17 3.13
282 1 31.84 34.34 39.67
283 1 14.41 17.74 14.43
284 1 9.4 1.78 29.53
285 1 8.29 29.61 6.81
286 1 7.13 17.36 -0.19
287 1 38.04 19.52 11.25
288 1 34.87 32.77 38.75
289 1 27.18 22.49 5.69
290 1 29.69 27.11 20.29
291 1 25.23 2.22 39.75
292 1 35.8 17.1 36.09
293 1 20.53 17.67 35.47
294 1 23.41 31.36 2.24
295 1 25.17 20.09 29.2
296 1 0.32 9.28 39.74
297 1 22.49 18.77 29.89
298 1 38.64 0.85 39.43
299 1 18.55 5.87 9.15
300 1 35.21 28.69 25.76
301 1 39.24 15.68 6.36
302 1 5.91 13.29 3.92
303 1 0.5 21.25 21.62
304 1 34.39 9.43 18.59
305 1 22.7 1.03 8.79
306 1 40.15 16.25 24.87
307 1 16.52 13.69 10.25
308 1 6.88 36.77 39.57
309 1 11.95 37.1 7.59
310 1 19.49 26.66 9.76
311 1 36.34 29.89 29.31
312 1 18.76 35.75 12.72
313 1 23.15 38.68 4.96
314 1 10.78 17.11 34.38
315 1 13.58 14.89 0.34
316 1 4.73 33.88 32.41
317 1 12.68 29.51 17.07
318 1 9.45 27 4.98
319 1 29.02 19.27 6.45
320 1 19.09 36.35 19.84
321 1 23.13 6.75 19.78
322 1 8.02 34.1 26.95
323 1 26.03 14.18 1.57
324 1 15.01 34.16 28.32
325 1 28.71 36.53 15.08
326 1 9.64 13.94 24.05
327 1 1.24 36.96 30.41
328 1 15.44 31.39 4.77
329 1 25.72 14.42 38.01
330 1 7.35 31.84 12.61
331 1 32.33 16.79 3.07
332 1 15.86 0.39 8.39
333 1 27.69 7.32 25.74
334 1 27.77 1.17 4.96
335 1 29.38 26.68 23.48
336 1 14.95 3.41 2.13
337 1 2.45 38.8 17.54
338 1 9.18 27.58 31.12
339 1 36.62 15.23 23.66
340 1 12.23 30.74 10.85
341 1 12.87 0.23 24.05
342 1 33.85 35.75 19.95
343 1 36.36 30.35 13.94
344 1 38.11 8.15 5.49
345 1 15.58 1.29 29.89
346 1 25.95 30.47 39.19
347 1 27.69 15.5 13.37
348 1 25.48 13.7 25.29
349 1 0.72 39.53 4.41
350 1 8.75 15.21 5.79
351 1 10.49 26.46 27.25
352 1 16.9 20.08 26.58
353 1 3.95 4.33 20.25
354 1 18.03 7.66 31.87
355 1 21.35 2.88 17.26
356 1 32.92 22.68 6.56
357 1 21.72 4.62 12.02
358 1 37.6 6.04 25.2
359 1 22.22 23.78 7.36
360 1 12.53 19.53 10.6
361 1 17.87 26.05 19.32
362 1 20.94 30.75 31.23
363 1 22.33 11.87 35.79
364 1 28.54 6.88 10.52
365 1 29.58 26.13 8.56
366 1 19.06 24.2 21.73
367 1 25.05 38.41 26.91
368 1 18.66 40.35 4.69
369 1 11.87 6.75 12.72
370 1 17.99 11.82 37.79
371 1 8.97 24.7 0.61
372 1 26.89 1.52 31.33
373 1 6.88 22.51 14.06
374 1 29.51 3.87 13.35
375 1 0.95 14.53 10
376 1 26.43 31.54 11.63
377 1 6.1 35.16 11.28
378 1 10.2 15.91 28.7
379 1 13.24 25.67 24.3
380 1 34.5 3.91 20.22
381 1 22.48 2.17 5.2
382 1 24.26 16.15 11.3
383 1 20.63 32.57 27.3
384 1 39.95 6.81 1.05
385 1 24.38 34.78 38.27
386 1 4.63 23.56 0.55
387 1 33.5 8.38 36.97
388 1 5.76 27.14 12.06
389 1 37.45 26.58 32.25
390 1 2.8 8.96 32.35
391 1 5.29 39.84 30.1
392 1 29.2 26.49 31.18
393 1 33.91 27.39 12.89
394 1 3.37 14.19 39.34
395 1 30.68 28.7 27
396 1 2.59 18.45 19.38
397 1 13.55 0.75 27.35
398 1 3.82 20.12 16.1
399 1 37.72 0.72 34.29
400 1 23.85 3.32 19.46
401 1 4.78 0.67 38.23
402 1 22.78 23.26 38.6
403 1 11.56 39.29 4.23
404 1 21.38 32.45 5.39
405 1 8.32 19.42 9.52
406 1 28.43 31.07 17.8
407 1 11.02 5.75 39.84
408 1 27.36 36.71 7.62
409 1 34.22 16.74 27.88
410 1 3.22 22.01 27.42
411 1 29.2 15.76 32.33
412 1 25.29 23.44 2.2
413 1 10.8 32.43 39.96
414 1 32.2 1.41 4.44
415 1 32.94 15.59 37.21
416 1 6.8 8.08 0.84
417 1 10.42 9.91 37.73
418 1 1.18 31.39 3.93
419 1 10.1 36.38 38.57
420 1 32.89 26.96 35.07
421 1 28.12 11.93 25.96
422 1 4.9 29.15 -0.25
423 1 2.21 27.99 3.72
424 1 11.33 3.94 25.55
425 1 3.3 30.26 10.78
426 1 11.57 27.26 19.31
427 1 21.79 32.67 13.3
428 1 4.96 26.53 33.78
429 1 33.41 32.87 18.46
430 1 13.92 30.37 20.3
431 1 16.91 3.5 11.57
432 1 -0.06 4.42 34.05
433 1 7.04 24.33 16.85
434 1 28.66 11.93 19.73
435 1 30.21 1.75 36.36
436 1 3.91 6.2 6.26
437 1 7.01 25.6 27.34
438 1 34 1.06 18.12
439 1 29.14 8.5 3.09
440 1 40.13 23.52 16.94
441 1 21.69 22.38 26.78
442 1 18.44 32.85 39.84
443 1 38.87 1.99 27.63
444 1 10.47 12.02 33.68
445 1 9.65 19.94 21.88
446 1 25.04 8.12 27.89
447 1 12.18 16.78 31.09
448 1 38.31 8.2 30.6
449 1 0.11 5.21 18.12
450 1 23.48 7.88 38.7
451 1 7.9 11.99 7.04
452 1 2.09 34.5 8.64
453 1 19 18.3 0.42
454 1 37.94 18.06 15.21
455 1 25.05 33.33 29.55
456 1 33.74 37.88 34.54
457 1 36.07 29.5 17.47
458 1 27.7 13.54 10.46
459 1 27.18 23.18 21.06
460 1 17.49 2.04 23.22
461 1 23.84 26.31 36.76
462 1 31.08 32.24 24.92
463 1 17.7 28.73 16.66
464 1 1.59 15.5 18.04
465 1 33.49 18.99 8.75
466 1 1.19 8.43 28.01
467 1 5.43 20.26 22.25
468 1 23.3 5.31 15.05
469 1 27.09 4.47 21.96
470 1 26.61 27.48 28.83
471 1 13 3.18 13.4
472 1 36.09 34.56 10.58
473 1 19.09 15.33 7.48
474 1 12.94 18.16 22.07
475 1 38.8 16.16 36.73
476 1 16.73 39.94 -0.46
477 1 3.64 12.56 9.42
478 1 27.64 3.31 18.29
479 1 15.58 12.36 4.52
480 1 15.37 11.18 18.19
481 1 37.52 11.23 14.94
482 1 37.16 2.3 10.01
483 1 36.19 9.86 21.99
484 1 36.38 21.09 4.76
485 1 38.15 12.94 25.35
486 1 15.1 29.65 24.64
487 1 16.54 29.12 38.85
488 1 33.86 11.39 14.4
489 1 27.99 18.55 9.87
490 1 0.66 1.26 8.28
491 1 29.89 33.84 29.75
492 1 6.64 33.3 6.74
493 1 31.47 0.39 11.25
494 1 8.76 15.96 10.74
495 1 39.6 15.8 21.04
496 1 22.38 28.55 19.85
497 1 25.87 6.23 5.4
498 1 36.24 26.67 38.61
499 1 23.05 8.79 7.01
500 1 32.05 4.16 8.87
501 1 35.3 13.36 38.03
502 1 39.91 25.91 36.45
503 1 32.17 17.27 31.82
504 1 29.99 21.54 20.57
505 1 9.39 0.57 34.17
506 1 22.12 17.22 13.03
507 1 15.23 16.27 24.39
508 1 26.32 25.89 13.26
509 1 39.25 3.46 1.34
510 1 32.56 10.28 7.96
511 1 25.76 14.8 34.79
512 1 32.12 5.38 36.94
513 1 17.74 15.37 14.87
514 1 21.93 3.26 25.26
515 1 24.05 0.48 36.27
516 1 8.2 19.02 33.92
517 1 33.07 25.88 24.79
518 1 12.54 0.52 32.8
519 1 18.5 6.34 23.21
520 1 35.93 10.26 34.79
521 1 19.33 11.86 6.94
522 1 1.63 5.31 25.43
523 1 30.62 36.78 30.77
524 1 12.25 26.79 13.74
525 1 21 1.47 13.99
526 1 22.24 29.36 34.11
527 1 29.05 1.74 0.24
528 1 19.34 25.14 39.77
529 1 12.9 25.42 35.42
530 1 4.1 20.69 33.31
531 1 35.38 5.64 9.17
532 1 5.01 34.03 23.36
533 1 15.7 10.01 7.1
534 1 25.95 19.48 24.73
535 1 11.15 4.16 21.43
536 1 1.47 3.23 13.72
537 1 26.54 36.76 17.48
538 1 7.65 30.6 27.73
539 1 18.59 3.05 3.32
540 1 6.92 36.14 15.67
541 1 12.72 36.21 32.72
542 1 16.33 26.24 14.35
543 1 21.66 12.61 26.18
544 1 15.72 32.37 10.71
545 1 27.57 15.75 4.97
546 1 20.18 39.13 18.44
547 1 18.77 17.09 4.74
548 1 12.75 14.08 17.89
549 1 10.71 37.26 35.13
550 1 20.88 32.12 9.94
551 1 8.69 0.06 9.54
552 1 1.58 12.61 26.42
553 1 10.29 22.73 13.14
554 1 23.31 25.7 4.97
555 1 36.7 30.78 5.26
556 1 5.6 28.71 23.76
557 1 13.04 7.91 15.46
558 1 40.24 33.53 34.5
559 1 39.7 18.36 34.25
560 1 23.52 22.84 21.14
561 1 32.82 27.9 5.02
562 1 1.52 33.77 27.04
563 1 31.48 18.68 13.1
564 1 34 24.07 34.55
565 1 34.72 25.03 30.45
566 1 18.92 5.7 16.54
567 1 15.26 40.2 16.97
568 1 24.55 16.8 26.26
569 1 17.59 18.03 31.75
570 1 12.08 27.38 38.42
571 1 31.42 21.91 35.27
572 1 9.68 6.93 36.96
573 1 22.93 15.19 2.53
574 1 11.83 24.38 2.24
575 1 16.02 12.44 31.42
576 1 20.24 10.7 20.15
577 1 37.38 17.37 40.63
578 1 3.74 17.41 22.49
579 1 23.21 9.86 23.99
580 1 2.49 36.56 38
581 1 20.51 1.54 22.62
582 1 8.23 33.44 33.15
583 1 30.93 8.12 14.85
584 1 36.35 3.92 37.65
585 1 5.57 10.63 28.64
586 1 30.24 22.84 4.6
587 1 3.24 15.97 7.43
588 1 22.64 0.7 27.09
589 1 1.64 40.37 27.74
590 1 30.53 35.28 3.5
591 1 25.55 4.7 2.53
592 1 22.04 29.56 12.29
593 1 3.42 8.76 2.28
594 1 16.37 37.65 7.87
595 1 20.65 12.75 2.9
596 1 8.07 20.49 2.6
597 1 20.04 24.72 28.2
598 1 29.75 0.33 16.1
599 1 31.36 33.09 8.02
600 1 8.6 10.56 2.65
601 1 20.55 33.93 33.71
602 1 23.11 -0.42 31.7
603 1 27.07 6.69 18.5
604 1 15.65 23.71 11.8
605 1 23.88 24.17 30.1
606 1 0.79 32.46 16.99
607 1 25.96 20.19 2.43
608 1 35.16 12.33 4.73
609 1 16.53 17.12 10.45
610 1 19.74 35.94 8.62
611 1 -0.24 28.29 28.3
612 1 33.15 4.39 12.64
613 1 24.27 18.59 33.59
614 1 0.3 9.61 23.54
615 1 5.52 10.89 34.71
616 1 9.85 26.26 34.42
617 1 25.54 37.74 39.13
618 1 4.11 29.65 5.81
619 1 30.86 22.72 31.07
620 1 39.54 34.54 23.24
621 1 15.03 9.34 12.11
622 1 21.93 38.49 9.53
623 1 18.21 19.2 16.65
624 1 38.71 32.83 14.49
625 1 37.74 36.38 31.43
626 1 7.57 2.2 1.07
627 1 12.27 10.05 1.53
628 1 18.32 19.55 12.51
629 1 12.49 24.81 16.57
630 1 35.07 31.62 22.85
631 1 4.91 19.68 30.45
632 1 11.36 2.92 36.19
633 1 26.76 35.53 1.29
634 1 1.13 14.55 14.77
635 1 8.2 25.14 37.83
636 1 -0.5 0.85 23.08
637 1 17.95 18.01 37.61
638 1 2.44 37.75 0.71
639 1 3.77 23.41 17.91
640 1 3.34 14.41 35.96
641 1 14.89 31.42 31.76
642 1 15.72 22.91 30.66
643 1 37.42 3.13 5.51
644 1 1.51 38.14 20.78
645 1 12.55 18.16 25.81
646 1 18.98 15.88 29.21
647 1 17.33 32.04 27.87
648 1 31.21 37.38 22.84
649 1 11.88 32.4 31
650 1 25.1 2.19 12.69
651 1 38.85 39.1 27.87
652 1 5.9 16.14 33.34
653 1 6.3 17.5 36.46
654 1 2.28 25.02 12.53
655 1 19.33 25.49 6.78
656 1 8.57 37.22 8.4
657 1 22 38.61 24.14
658 1 35.63 3.23 2.15
659 1 37.35 22.64 9.99
660 1 25.46 28.22 33.18
661 1 13.99 4.21 9.07
662 1 9.04 40.64 37.59
663 1 17.46 6.49 27.93
664 1 1.42 6.14 30.2
665 1 25.82 28.28 10.33
666 1 30.71 30.2 -0.02
667 1 8.05 29.32 0.62
668 1 6.49 3.17 6.65
669 1 7.77 39.88 26.03
670 1 28.53 12.14 30.96
671 1 6.25 12.64 39.55
672 1 3.78 7.96 25.83
673 1 28.69 29.58 6.61
674 1 5.32 18.55 8.6
675 1 5.3 11.44 14.19
676 1 39 12.03 36.99
677 1 11.08 32.51 19.12
678 1 38.48 1.03 20.34
679 1 38.47 11.31 10.12
680 1 3.65 20.3 11.99
681 1 27.18 11.39 3.4
682 1 29.61 20.72 38.86
683 1 31.88 4.82 24.75
684 1 14.52 36.61 25.66
685 1 21.68 19.96 24.58
686 1 1.2 13.59 23.16
687 1 37.71 5.97 35.28
688 1 19.81 22.04 37.54
689 1 40.67 27.07 10.14
690 1 38.57 13.96 13.75
691 1 18.15 17.19 21.63
692 1 3.76 27.51 30.32
693 1 11.39 25.09 7.96
694 1 28.95 22.02 13.33
695 1 31.72 35.46 35.33
696 1 15.17 6.03 23.94
697 1 9.63 9.42 22.18
698 1 27.76 4.1 38.61
699 1 27.37 37.46 11.07
700 1 35.69 15.24 6.39
701 1 21.92 33.09 36.84
702 1 4.79 15.51 13.28
703 1 9.31 26.44 22.8
704 1 30.14 38.31 6.98
705 1 4.33 6.66 13.77
706 1 3.66 27.15 37.83
707 1 0.44 24.06 29.62
708 1 35.4 9.59 9.8
709 1 33.77 39.44 21.41
710 1 29.2 18.74 24.38
711 1 34.14 30 7.36
712 1 16.02 4.37 6.43
713 1 35.75 39.41 40.58
714 1 15.32 11.84 23.24
715 1 32.52 24.39 20.97
716 1 11.45 2.9 7.16
717 1 7.07 34.28 36.04
718 1 11.41 8.83 7.57
719 1 29.29 27.79 16.55
720 1 2.41 9.16 16.14
721 1 13.14 38.07 12.01
722 1 37.45 14.26 18.3
723 1 34.64 18.37 16.65
724 1 29.26 34.28 33.46
725 1 13.67 19.83 3.04
726 1 19.64 2.6 32.95
727 1 23.61 23.55 11.34
728 1 6.87 22.5 36.5
729 1 36.78 28.34 22.96
730 1 11.3 13.98 9.84
731 1 20.82 19.73 9.16
732 1 12.65 12.61 6.16
733 1 9.25 7.81 25.28
734 1 25.4 29.36 5.84
735 1 17.86 9.06 4.45
736 1 35.84 40.51 26.06
737 1 26.97 21.28 31.59
738 1 39.94 38.14 24.86
739 1 3.16 17.07 2.49
740 1 14.08 15.4 36.99
741 1 26.1 13.88 29.68
742 1 26.36 20 20.56
743 1 12.02 6.35 27.65
744 1 11.21 19.14 15.27
745 1 35.86 22.93 26.81
746 1 32.26 12.62 2.68
747 1 29.36 4.91 6.86
748 1 20.14 7.97 29.32
749 1 25.53 11.2 36.18
750 1 30.36 14.25 24.79
751 1 29.84 38.37 39.29
752 1 15.79 36.4 4.26
753 1 32.59 14.17 10.29
754 1 13.89 34.54 15.42
755 1 12.13 33.62 7.27
756 1 25.86 23.81 33.97
757 1 18.4 31.27 34.96
758 1 6.58 40.49 17.57
759 1 5.64 39.86 23.05
760 1 25.32 33 16.24
761 1 0.98 10.99 12.21
762 1 32.86 23.75 12.41
763 1 32.91 1.3 26.94
764 1 9.46 8.66 31.47
765 1 17.49 15.53 1.82
766 1 8.17 18.16 15.3
767 1 4.84 30.63 26.32
768 1 6.75 37.1 30.8
769 1 7.16 5.72 15.74
770 1 20.09 17.82 19.18
771 1 1.02 27.99 32.54
772 1 21.44 1.28 38.4
773 1 21.06 14.62 37.08
774 1 27.82 18.99 15.96
775 1 33.51 21.46 22.82
776 1 8.29 2.79 17.09
777 1 18.14 11.41 28.62
778 1 17.94 28.54 32.73
779 1 36.1 9.54 40.1
780 1 36.55 2.62 22.97
781 1 27.29 10.41 39.35
782 1 22.04 37.76 2.02
783 1 23.01 30.08 16.58
784 1 6.34 15.31 21.61
785 1 7.3 22.39 7.74
786 1 38 5.77 21.04
787 1 32.93 12.85 26.58
788 1 22.43 15.36 16.72
789 1 18.54 2.38 8.35
790 1 0.62 31.88 23.84
791 1 39.56 30.3 21.7
792 1 7.56 11.78 25.2
793 1 16.05 3.98 26.72
794 1 24.33 36.16 13.16
795 1 26.38 31.24 35.77
796 1 14.94 26.46 -0.44
797 1 3.53 28 19.79
798 1 11.94 32.27 25.88
799 1 34.59 15.06 19.23
800 1 3.51 10.62 24.22
801 1 13.18 21.59 35.52
802 1 19.95 13.15 16.23
803 1 24.48 9.63 19.58
804 1 37.7 34.42 19.19
805 1 22.84 19.59 5.52
806 1 34.62 36.75 12.26
807 1 10.33 21.85 25.15
808 1 21.51 29.7 7.23
809 1 34.05 3 30.58
810 1 12.43 29.67 5.59
811 1 18.94 21.82 29.31
812 1 39.21 17.7 4
813 1 7.04 2.97 37.09
814 1 30.87 10.8 22.09
815 1 33.54 7.16 23.15
816 1 32.82 32.27 11.47
817 1 21.8 14.54 21.61
818 1 38.83 6.69 13.68
819 1 30.37 39.05 18.66
820 1 31.21 15.08 13.79
821 1 1.07 11.97 35.04
822 1 26.02 35.8 35.47
823 1 27.64 33.32 8.04
824 1 39.57 36.88 4.39
825 1 14.48 30.97 36.87
826 1 36.86 27.04 8.96
827 1 34.73 26.27 19.55
828 1 29.24 29.12 10.86
829 1 8.35 39.9 13.92
830 1 5.43 5.1 31.85
831 1 18.36 22.31 5.89
832 1 2.46 27.35 16.36
833 1 21.76 37.05 27.45
834 1 29.32 17.11 2.28
835 1 3.58 21.98 3.09
836 1 10.61 9.17 10.69
837 1 25.15 17.54 6.05
838 1 3.4 22.81 7.03
839 1 16.12 23.66 38.29
840 1 8.67 4.79 31.8
841 1 27.82 0.02 20.45
842 1 4.46 2.44 29.46
843 1 39.11 22.69 36.33
844 1 4.26 2.45 34.43
845 1 13.47 3.5 30.9
846 1 26.92 22.55 26.54
847 1 5.66 30.07 30.65
848 1 31.58 35.68 25.46
849 1 31.23 5.65 27.78
850 1 8.76 19.49 28.61
851 1 24.13 8.02 2.3
852 1 8.27 6.8 4.93
853 1 15.31 34.36 37.63
854 1 3.96 35.82 26.97
855 1 24.95 4.01 29.96
856 1 26.54 25.95 19.15
857 1 17.76 29.23 5.35
858 1 16.95 21.79 0.78
859 1 17.52 39.02 13.01
860 1 20.5 22.86 10.41
861 1 27.67 27.07 2.78
862 1 37.1 31.02 2.03
863 1 37.17 2.24 16.34
864 1 24.51 34.69 10.28
865 1 17.38 13.41 21.4
866 1 38 9.37 17.94
867 1 35.67 25.27 5.3
868 1 22.66 4.47 0.97
869 1 20.06 28.17 27.42
870 1 27.33 2.38 9.79
871 1 36.4 10.73 31.42
872 1 0.53 9.45 6.96
873 1 12.89 9.03 25.13
874 1 37.5 23.54 21.33
875 1 7.19 28.87 19.11
876 1 21.45 32.81 22.71
877 1 8.76 8.3 13.51
878 1 10.24 31.46 3.73
879 1 15.93 9.7 35.82
880 1 14.92 19.46 39.91
881 1 13.02 22.03 27.3
882 1 34.57 1.59 34.73
883 1 0.5 21.04 30.77
884 1 24.84 32.67 4.97
885 1 30.96 4.24 17.34
886 1 23.63 8.84 32.7
887 1 6.84 3.83 26.13
888 1 31.57 9.23 27.06
889 1 14.99 35.15 0.07
890 1 36.29 40.01 8.22
891 1 18 36.86 35.66
892 1 11.5 29.22 0.37
893 1 35.18 36.03 24.88
894 1 14.49 9.41 27.73
895 1 10.12 12.91 0.99
896 1 11.91 29.4 27.3
897 1 25.51 28.68 14.56
898 1 29.32 12.95 35.59
899 1 2.96 0.59 0.53
900 1 5.47 5.35 9.88
901 1 8.93 39.33 1.78
902 1 39.68 38.49 12.33
903 1 3.78 1.24 11.85
904 1 29.54 33.76 11.99
905 1 7.48 6.16 28.8
906 1 10.83 33.63 36.96
907 1 22.03 19.06 21.39
908 1 31.68 31 3.71
909 1 35.32 0.3 30.88
910 1 9.93 35.42 14.85
911 1 21.01 10.66 12.97
912 1 22.54 21.62 33.81
913 1 12.48 12.46 25.15
914 1 0.64 27.93 39.01
915 1 13.88 27.29 3.8
916 1 13.03 20.93 19.25
917 1 5.7 37.48 34.09
918 1 2.27 35.08 14.29
919 1 21.75 26.44 13.48
920 1 10.66 11.35 17.49
921 1 36.67 34.72 27.69
922 1 8.23 22.8 33.36
923 1 4.79 4.05 3.48
924 1 35.61 35 35.21
925 1 31.38 37.67 10.06
926 1 26.44 35.58 27.52
927 1 25.53 4.47 8.03
928 1 38.81 33.08 31.55
929 1 29.62 39.68 34.32
930 1 0.76 3.88 10.61
931 1 24.06 30.13 24.84
932 1 18.77 8.38 37.02
933 1 2.81 24.14 24.45
934 1 11.33 1.25 19.69
935 1 1.61 26.53 6.48
936 1 9.52 29.81 35.98
937 1 7.83 31.75 20.77
938 1 9.67 23.93 20.57
939 1 33.96 16.95 24.79
940 1 37.55 37.31 37.17
941 1 6.2 24.19 31.13
942 1 17.79 4.35 30.56
943 1 13.51 20.25 30.45
944 1 14.76 12.48 13.13
945 1 32.56 27.52 30.41
946 1 35.81 40.1 4.85
947 1 39.01 25.43 27.07
948 1 22.8 5.53 32.22
949 1 2.35 39.55 32.5
950 1 3.31 31.51 34.19
951 1 40.63 37.01 15.9
952 1 18.43 35.86 30.77
953 1 37.01 39.18 15.57
954 1 6.74 6.26 21.64
955 1 5.22 24.94 22.53
956 1 25.2 11.08 13.98
957 1 14.66 -0.14 5
958 1 14.96 8.38 20.32
959 1 1.89 23.03 10.1
960 1 33.01 11.23 39.32
961 1 32.68 6.79 32.04
962 1 6.25 25.81 3.82
963 1 18.37 31.97 14.57
964 1 9.74 30.21 22.71
965 1 3.09 1.52 19.38
966 1 33.98 37.34 5.63
967 1 32.19 28.35 15.8
968 1 24.4 15.49 19.39

52
examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt Normal file
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# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
# write_restart restart_longrun
# write_data restart_longrun.data

BIN
examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz Normal file
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Binary file not shown.

175
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 Normal file
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
1 by 1 by 1 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 12167 5832
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 723.60507 -17175.571 0.80366765 76 48
200 736.71277 -12961.963 0.80366765 84 64
Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
Other | | 0.04545 | | | 0.04
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6928101
Ave neighs/atom = 196.821
Ave special neighs/atom = 9.83727
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:43

175
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 Normal file
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
2 by 1 by 2 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 4508 1620
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 724.40407 -17166.729 0.80366765 76 49
200 737.28582 -12968.224 0.80366765 84 65
Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
Other | | 0.03995 | | | 0.08
Nlocal: 8800 ave 8913 max 8652 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 18366 ave 18461 max 18190 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6928132
Ave neighs/atom = 196.822
Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:52

35
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map Normal file
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@ -0,0 +1,35 @@
this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
10
1
EdgeIDs
16
8
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18

189
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template Normal file
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@ -0,0 +1,189 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 3 16
9 2 3 17
10 2 3 18
11 1 8 9
12 6 9 10
13 2 9 13
14 2 9 14
15 7 10 11
16 5 10 12
17 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 2 2 3 16
14 1 2 3 17
15 1 2 3 18
16 1 16 3 17
17 1 16 3 18
18 3 17 3 18
19 12 8 9 10
20 1 8 9 13
21 1 8 9 14
22 13 13 9 10
23 13 14 9 10
24 3 13 9 14
25 10 9 10 11
26 8 9 10 12
27 20 1 10 9
28 21 11 10 12
29 22 1 10 11
30 23 1 10 12
31 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 26 1 2 3 16
20 27 1 2 3 17
21 27 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 14 8 9 10 11
29 12 8 9 10 12
30 28 8 9 10 1
31 15 13 9 10 11
32 13 13 9 10 12
33 29 13 9 10 1
34 15 14 9 10 11
35 13 14 9 10 12
36 29 14 9 10 1
37 10 9 10 12 15
38 11 11 10 12 15
39 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

160
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template Normal file
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@ -0,0 +1,160 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 2
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 12 1 2
2 4 1 4
3 4 1 5
4 1 2 3
5 2 2 6
6 2 2 7
7 1 3 16
8 2 3 17
9 2 3 18
10 1 8 9
11 6 9 10
12 2 9 13
13 2 9 14
14 7 10 11
15 5 10 12
16 8 12 15
Angles
1 6 2 1 4
2 6 2 1 5
3 7 4 1 5
4 24 1 2 3
5 5 1 2 6
6 5 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 2 2 3 16
11 1 2 3 17
12 1 2 3 18
13 1 16 3 17
14 1 16 3 18
15 3 17 3 18
16 12 8 9 10
17 1 8 9 13
18 1 8 9 14
19 13 13 9 10
20 13 14 9 10
21 3 13 9 14
22 10 9 10 11
23 8 9 10 12
24 21 11 10 12
25 11 10 12 15
Dihedrals
1 31 4 1 2 3
2 32 4 1 2 6
3 32 4 1 2 7
4 31 5 1 2 3
5 32 5 1 2 6
6 32 5 1 2 7
7 33 1 2 3 16
8 1 1 2 3 17
9 1 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 14 8 9 10 11
17 12 8 9 10 12
18 15 13 9 10 11
19 13 13 9 10 12
20 15 14 9 10 11
21 13 14 9 10 12
22 10 9 10 12 15
23 11 11 10 12 15
Impropers
1 1 2 1 4 5
2 9 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

32
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map Normal file
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@ -0,0 +1,32 @@
this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
4
12
EdgeIDs
8
3
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15

131
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template Normal file
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@ -0,0 +1,131 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 11
13 3
14 3
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 5
3 11 1 10
4 1 2 3
5 2 2 6
6 2 2 7
7 13 4 12
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 13 15 12
Angles
1 14 2 1 5
2 15 2 1 10
3 17 5 1 10
4 18 1 2 3
5 19 1 2 6
6 19 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 12 8 9 10
11 1 8 9 13
12 1 8 9 14
13 13 13 9 10
14 13 14 9 10
15 3 13 9 14
16 10 9 10 11
17 20 1 10 9
18 22 1 10 11
19 25 15 12 4
Dihedrals
1 16 5 1 2 3
2 17 5 1 2 6
3 17 5 1 2 7
4 18 10 1 2 3
5 19 10 1 2 6
6 19 10 1 2 7
7 20 2 1 10 9
8 21 2 1 10 11
9 23 5 1 10 9
10 24 5 1 10 11
11 14 8 9 10 11
12 28 8 9 10 1
13 15 13 9 10 11
14 29 13 9 10 1
15 15 14 9 10 11
16 29 14 9 10 1
Impropers
1 10 2 1 5 10
2 11 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

158
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template Normal file
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@ -0,0 +1,158 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 5 10 12
14 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 12 8 9 10
14 1 8 9 13
15 1 8 9 14
16 13 13 9 10
17 13 14 9 10
18 3 13 9 14
19 10 9 10 11
20 8 9 10 12
21 20 1 10 9
22 21 11 10 12
23 22 1 10 11
24 23 1 10 12
25 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 14 8 9 10 11
20 12 8 9 10 12
21 28 8 9 10 1
22 15 13 9 10 11
23 13 13 9 10 12
24 29 13 9 10 1
25 15 14 9 10 11
26 13 14 9 10 12
27 29 14 9 10 1
28 10 9 10 12 15
29 11 11 10 12 15
30 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

50
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon Normal file
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@ -0,0 +1,50 @@
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
# write_restart restart_longrun
# write_data restart_longrun.data

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 Normal file
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@ -0,0 +1,370 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299879 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225228 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.80615652 0.0034851739 1 1
3750 297.55588 -0.49626039 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37593 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779678 0.0034851739 1 1
4200 241.30632 -33.371788 0.0034851739 1 1
4250 242.17258 -9.986197 0.0034851739 1 1
4300 300.85311 -7.9244294 0.0034851739 1 1
4350 273.15684 -21.257283 0.0034851739 1 1
4400 305.77463 -5.8720722 0.0034851739 1 1
4450 314.97697 45.0373 0.0034851739 1 1
4500 310.77723 16.958773 0.0034851739 1 1
4550 302.1742 12.156862 0.0034851739 1 1
4600 319.74799 6.84889 0.0034851739 1 1
4650 270.86805 -13.767905 0.0034851739 1 1
4700 249.81731 -31.197487 0.0034851739 1 1
4750 285.86481 -9.8916364 0.0034851739 1 1
4800 233.98321 7.1338571 0.0034851739 1 1
4850 302.60551 49.262889 0.0034851739 1 1
4900 316.55056 34.663247 0.0034851739 1 1
4950 357.32741 11.583006 0.0034851739 1 1
5000 400.21045 -8.1781061 0.0034851739 1 1
5050 390.01845 -20.490275 0.0034851739 1 1
5100 378.84247 -41.328757 0.0034851739 1 1
5150 324.02038 -15.023862 0.0034851739 1 1
5200 262.08429 10.937354 0.0034851739 1 1
5250 255.75508 16.381455 0.0034851739 1 1
5300 277.84989 40.68232 0.0034851739 1 1
5350 302.92832 9.1989494 0.0034851739 1 1
5400 283.7196 -1.6584671 0.0034851739 1 1
5450 300.71266 -4.7030295 0.0034851739 1 1
5500 343.5499 -0.30550044 0.0034851739 1 1
5550 369.51271 21.691649 0.0034851739 1 1
5600 372.69789 -38.67994 0.0034851739 1 1
5650 327.41266 11.352137 0.0034851739 1 1
5700 278.98614 -23.827304 0.0034851739 1 1
5750 308.30054 -20.756187 0.0034851739 1 1
5800 341.45594 28.058441 0.0034851739 1 1
5850 322.97844 -10.731921 0.0034851739 1 1
5900 304.53591 32.825279 0.0034851739 1 1
5950 287.1752 -36.780091 0.0034851739 1 1
6000 296.52681 18.781896 0.0034851739 1 1
6050 314.25442 15.992829 0.0034851739 1 1
6100 313.86576 3.4342714 0.0034851739 1 1
6150 325.64196 32.392039 0.0034851739 1 1
6200 367.42931 -27.160706 0.0034851739 1 1
6250 369.30798 39.020934 0.0034851739 1 1
6300 328.92285 -23.175157 0.0034851739 1 1
6350 305.63077 4.9024453 0.0034851739 1 1
6400 241.70341 -13.676629 0.0034851739 1 1
6450 265.66717 2.40612 0.0034851739 1 1
6500 249.36037 13.420255 0.0034851739 1 1
6550 294.53814 10.853462 0.0034851739 1 1
6600 308.2025 18.995308 0.0034851739 1 1
6650 305.43797 -49.56785 0.0034851739 1 1
6700 320.27344 11.336281 0.0034851739 1 1
6750 321.78666 -23.463899 0.0034851739 1 1
6800 303.40388 7.6224553 0.0034851739 1 1
6850 297.18966 51.52256 0.0034851739 1 1
6900 284.18909 -8.4947203 0.0034851739 1 1
6950 331.03663 13.233655 0.0034851739 1 1
7000 311.37928 -43.265479 0.0034851739 1 1
7050 286.81661 -14.174683 0.0034851739 1 1
7100 302.84119 12.048954 0.0034851739 1 1
7150 297.19357 -43.111968 0.0034851739 1 1
7200 332.47359 26.048249 0.0034851739 1 1
7250 262.70677 41.176242 0.0034851739 1 1
7300 250.61405 -23.413982 0.0034851739 1 1
7350 296.91117 35.88133 0.0034851739 1 1
7400 245.09229 -13.447194 0.0034851739 1 1
7450 272.28131 -23.322585 0.0034851739 1 1
7500 209.04985 13.871239 0.0034851739 1 1
7550 255.00955 4.9325621 0.0034851739 1 1
7600 312.30937 -37.368274 0.0034851739 1 1
7650 305.65903 55.245496 0.0034851739 1 1
7700 325.09504 -18.347711 0.0034851739 1 1
7750 363.28282 -22.479686 0.0034851739 1 1
7800 350.17429 26.849547 0.0034851739 1 1
7850 271.70853 -17.764575 0.0034851739 1 1
7900 272.66484 -11.701967 0.0034851739 1 1
7950 298.60202 -12.765675 0.0034851739 1 1
8000 274.58852 49.641532 0.0034851739 1 1
8050 304.72347 -0.55414183 0.0034851739 1 1
8100 328.30757 -39.861301 0.0034851739 1 1
8150 406.67601 2.8999409 0.0034851739 1 1
8200 332.20083 -51.217399 0.0034851739 1 1
8250 354.50609 53.128769 0.0034851739 1 1
8300 337.2758 20.68562 0.0034851739 1 1
8350 361.89708 -54.185869 0.0034851739 1 1
8400 305.63496 24.058529 0.0034851739 1 1
8450 303.27461 4.304683 0.0034851739 1 1
8500 253.53694 -10.909021 0.0034851739 1 1
8550 277.03017 23.241479 0.0034851739 1 1
8600 291.41844 -22.240665 0.0034851739 1 1
8650 307.85368 31.919587 0.0034851739 1 1
8700 309.19724 0.53529642 0.0034851739 1 1
8750 354.6583 11.565515 0.0034851739 1 1
8800 329.78598 19.5996 0.0034851739 1 1
8850 240.79198 21.803515 0.0034851739 1 1
8900 318.40749 -59.816923 0.0034851739 1 1
8950 308.47211 -57.808635 0.0034851739 1 1
9000 271.51207 50.943482 0.0034851739 1 1
9050 249.4005 6.7529187 0.0034851739 1 1
9100 221.8772 47.196092 0.0034851739 1 1
9150 297.9351 4.0058184 0.0034851739 1 1
9200 274.85051 -24.774393 0.0034851739 1 1
9250 336.04757 5.3799028 0.0034851739 1 1
9300 380.44956 -22.389381 0.0034851739 1 1
9350 336.9824 23.050616 0.0034851739 1 1
9400 304.46425 32.530218 0.0034851739 1 1
9450 317.55591 -22.265425 0.0034851739 1 1
9500 323.70901 -7.0159787 0.0034851739 1 1
9550 316.07308 28.062131 0.0034851739 1 1
9600 262.74608 -0.78519192 0.0034851739 1 1
9650 271.55045 -21.430123 0.0034851739 1 1
9700 239.6022 14.483637 0.0034851739 1 1
9750 338.1437 -0.72765302 0.0034851739 1 1
9800 334.50189 19.495144 0.0034851739 1 1
9850 354.87554 19.272719 0.0034851739 1 1
9900 334.02141 -22.393457 0.0034851739 1 1
9950 293.63651 19.178873 0.0034851739 1 1
10000 319.81736 21.904414 0.0034851739 1 1
Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
Other | | 0.01666 | | | 0.90
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 Normal file
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299878 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225229 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.8061567 0.0034851739 1 1
3750 297.55588 -0.49626022 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37594 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779683 0.0034851739 1 1
4200 241.30632 -33.371789 0.0034851739 1 1
4250 242.17258 -9.9861962 0.0034851739 1 1
4300 300.85311 -7.924429 0.0034851739 1 1
4350 273.15684 -21.257282 0.0034851739 1 1
4400 305.77464 -5.8720712 0.0034851739 1 1
4450 314.97697 45.037299 0.0034851739 1 1
4500 310.77723 16.958771 0.0034851739 1 1
4550 302.17421 12.156862 0.0034851739 1 1
4600 319.74799 6.8488914 0.0034851739 1 1
4650 270.86805 -13.767907 0.0034851739 1 1
4700 249.81731 -31.197484 0.0034851739 1 1
4750 285.86481 -9.8916332 0.0034851739 1 1
4800 233.98321 7.1338518 0.0034851739 1 1
4850 302.60551 49.262886 0.0034851739 1 1
4900 316.55055 34.663238 0.0034851739 1 1
4950 357.32741 11.583013 0.0034851739 1 1
5000 400.21044 -8.1780861 0.0034851739 1 1
5050 390.01845 -20.490268 0.0034851739 1 1
5100 378.84249 -41.328772 0.0034851739 1 1
5150 324.02039 -15.023852 0.0034851739 1 1
5200 262.08427 10.937367 0.0034851739 1 1
5250 255.75506 16.381495 0.0034851739 1 1
5300 277.84991 40.682283 0.0034851739 1 1
5350 302.92834 9.1989644 0.0034851739 1 1
5400 283.71964 -1.6583895 0.0034851739 1 1
5450 300.71261 -4.703054 0.0034851739 1 1
5500 343.54987 -0.30546396 0.0034851739 1 1
5550 369.51272 21.691639 0.0034851739 1 1
5600 372.69786 -38.679919 0.0034851739 1 1
5650 327.41256 11.352201 0.0034851739 1 1
5700 278.9861 -23.82728 0.0034851739 1 1
5750 308.30037 -20.756238 0.0034851739 1 1
5800 341.4559 28.058314 0.0034851739 1 1
5850 322.9786 -10.731862 0.0034851739 1 1
5900 304.53598 32.825105 0.0034851739 1 1
5950 287.17515 -36.780057 0.0034851739 1 1
6000 296.52688 18.782156 0.0034851739 1 1
6050 314.25411 15.99272 0.0034851739 1 1
6100 313.86572 3.4344108 0.0034851739 1 1
6150 325.64197 32.39212 0.0034851739 1 1
6200 367.4298 -27.161154 0.0034851739 1 1
6250 369.30937 39.020881 0.0034851739 1 1
6300 328.92245 -23.175612 0.0034851739 1 1
6350 305.6293 4.9011587 0.0034851739 1 1
6400 241.70456 -13.675247 0.0034851739 1 1
6450 265.66574 2.4049735 0.0034851739 1 1
6500 249.3592 13.420453 0.0034851739 1 1
6550 294.5367 10.856753 0.0034851739 1 1
6600 308.20246 18.992923 0.0034851739 1 1
6650 305.43756 -49.57151 0.0034851739 1 1
6700 320.27395 11.339101 0.0034851739 1 1
6750 321.7875 -23.463361 0.0034851739 1 1
6800 303.40316 7.6256997 0.0034851739 1 1
6850 297.18652 51.52186 0.0034851739 1 1
6900 284.19084 -8.496294 0.0034851739 1 1
6950 331.04173 13.227745 0.0034851739 1 1
7000 311.38027 -43.26105 0.0034851739 1 1
7050 286.82046 -14.171194 0.0034851739 1 1
7100 302.81691 12.058085 0.0034851739 1 1
7150 297.18018 -43.110658 0.0034851739 1 1
7200 332.46131 26.051496 0.0034851739 1 1
7250 262.72288 41.161451 0.0034851739 1 1
7300 250.62739 -23.440907 0.0034851739 1 1
7350 296.92141 35.869216 0.0034851739 1 1
7400 245.06807 -13.467896 0.0034851739 1 1
7450 272.2659 -23.292836 0.0034851739 1 1
7500 209.05776 13.888665 0.0034851739 1 1
7550 255.03716 4.9662624 0.0034851739 1 1
7600 312.26011 -37.350427 0.0034851739 1 1
7650 305.5823 55.208039 0.0034851739 1 1
7700 325.13382 -18.370791 0.0034851739 1 1
7750 363.24898 -22.473126 0.0034851739 1 1
7800 350.19254 26.792307 0.0034851739 1 1
7850 271.76418 -17.843445 0.0034851739 1 1
7900 272.70301 -11.709349 0.0034851739 1 1
7950 298.5993 -12.736235 0.0034851739 1 1
8000 274.52611 49.657345 0.0034851739 1 1
8050 304.73711 -0.52485689 0.0034851739 1 1
8100 328.29239 -39.901891 0.0034851739 1 1
8150 406.52096 2.8669076 0.0034851739 1 1
8200 332.17309 -51.168754 0.0034851739 1 1
8250 354.68419 53.003157 0.0034851739 1 1
8300 337.28934 20.766408 0.0034851739 1 1
8350 361.81133 -54.159227 0.0034851739 1 1
8400 305.59597 24.011667 0.0034851739 1 1
8450 303.25823 4.423341 0.0034851739 1 1
8500 253.50747 -11.026949 0.0034851739 1 1
8550 277.13504 23.204625 0.0034851739 1 1
8600 291.40211 -22.253861 0.0034851739 1 1
8650 307.93765 32.14162 0.0034851739 1 1
8700 309.1529 0.36279434 0.0034851739 1 1
8750 355.10326 11.677219 0.0034851739 1 1
8800 330.21328 19.235269 0.0034851739 1 1
8850 241.29109 21.707386 0.0034851739 1 1
8900 319.15363 -60.010115 0.0034851739 1 1
8950 308.88552 -57.637014 0.0034851739 1 1
9000 272.22373 51.15837 0.0034851739 1 1
9050 248.84947 7.3390565 0.0034851739 1 1
9100 221.91564 48.387079 0.0034851739 1 1
9150 298.03506 2.9058639 0.0034851739 1 1
9200 274.25114 -24.597819 0.0034851739 1 1
9250 334.08373 5.1079577 0.0034851739 1 1
9300 383.07285 -23.274763 0.0034851739 1 1
9350 335.00581 20.94212 0.0034851739 1 1
9400 309.23862 34.074744 0.0034851739 1 1
9450 312.62262 -28.468057 0.0034851739 1 1
9500 324.54274 2.851136 0.0034851739 1 1
9550 313.32781 22.468182 0.0034851739 1 1
9600 269.04372 4.064934 0.0034851739 1 1
9650 270.98476 -21.520127 0.0034851739 1 1
9700 236.8736 16.250728 0.0034851739 1 1
9750 333.94686 1.6864148 0.0034851739 1 1
9800 330.91875 12.150018 0.0034851739 1 1
9850 343.8603 25.338853 0.0034851739 1 1
9900 330.93364 -28.292992 0.0034851739 1 1
9950 291.25518 25.795948 0.0034851739 1 1
10000 319.25565 25.323846 0.0034851739 1 1
Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
Other | | 0.02359 | | | 0.66
Nlocal: 11 ave 44 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 33 ave 44 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 205.75 ave 823 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

35
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map Normal file
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@ -0,0 +1,35 @@
this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
10
1
EdgeIDs
16
8
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18

189
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template Normal file
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@ -0,0 +1,189 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 3 16
9 1 3 17
10 1 3 18
11 2 8 9
12 4 9 10
13 1 9 13
14 1 9 14
15 5 10 11
16 3 10 12
17 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 3 2 3 16
14 2 2 3 17
15 2 2 3 18
16 2 16 3 17
17 2 16 3 18
18 1 17 3 18
19 8 8 9 10
20 2 8 9 13
21 2 8 9 14
22 23 13 9 10
23 23 14 9 10
24 1 13 9 14
25 6 9 10 11
26 4 9 10 12
27 24 1 10 9
28 25 11 10 12
29 26 1 10 11
30 27 1 10 12
31 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 29 1 2 3 16
20 30 1 2 3 17
21 30 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 10 8 9 10 11
29 8 8 9 10 12
30 31 8 9 10 1
31 11 13 9 10 11
32 9 13 9 10 12
33 32 13 9 10 1
34 11 14 9 10 11
35 9 14 9 10 12
36 32 14 9 10 1
37 6 9 10 12 15
38 7 11 10 12 15
39 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

160
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template Normal file
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@ -0,0 +1,160 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 7
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 14 1 2
2 10 1 4
3 10 1 5
4 2 2 3
5 1 2 6
6 1 2 7
7 2 3 16
8 1 3 17
9 1 3 18
10 2 8 9
11 4 9 10
12 1 9 13
13 1 9 14
14 5 10 11
15 3 10 12
16 6 12 15
Angles
1 15 2 1 4
2 15 2 1 5
3 16 4 1 5
4 28 1 2 3
5 14 1 2 6
6 14 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 3 2 3 16
11 2 2 3 17
12 2 2 3 18
13 2 16 3 17
14 2 16 3 18
15 1 17 3 18
16 8 8 9 10
17 2 8 9 13
18 2 8 9 14
19 23 13 9 10
20 23 14 9 10
21 1 13 9 14
22 6 9 10 11
23 4 9 10 12
24 25 11 10 12
25 7 10 12 15
Dihedrals
1 34 4 1 2 3
2 35 4 1 2 6
3 35 4 1 2 7
4 34 5 1 2 3
5 35 5 1 2 6
6 35 5 1 2 7
7 36 1 2 3 16
8 12 1 2 3 17
9 12 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 10 8 9 10 11
17 8 8 9 10 12
18 11 13 9 10 11
19 9 13 9 10 12
20 11 14 9 10 11
21 9 14 9 10 12
22 6 9 10 12 15
23 7 11 10 12 15
Impropers
1 6 2 1 4 5
2 11 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

32
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map Normal file
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@ -0,0 +1,32 @@
this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
4
12
EdgeIDs
8
3
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15

131
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template Normal file
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@ -0,0 +1,131 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 11
13 4
14 4
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 5
3 13 1 10
4 2 2 3
5 1 2 6
6 1 2 7
7 15 4 12
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 15 15 12
Angles
1 17 2 1 5
2 18 2 1 10
3 20 5 1 10
4 21 1 2 3
5 22 1 2 6
6 22 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 8 8 9 10
11 2 8 9 13
12 2 8 9 14
13 23 13 9 10
14 23 14 9 10
15 1 13 9 14
16 6 9 10 11
17 24 1 10 9
18 26 1 10 11
19 29 15 12 4
Dihedrals
1 19 5 1 2 3
2 20 5 1 2 6
3 20 5 1 2 7
4 21 10 1 2 3
5 22 10 1 2 6
6 22 10 1 2 7
7 23 2 1 10 9
8 24 2 1 10 11
9 26 5 1 10 9
10 27 5 1 10 11
11 10 8 9 10 11
12 31 8 9 10 1
13 11 13 9 10 11
14 32 13 9 10 1
15 11 14 9 10 11
16 32 14 9 10 1
Impropers
1 12 2 1 5 10
2 13 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

158
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template Normal file
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@ -0,0 +1,158 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 3 10 12
14 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 8 8 9 10
14 2 8 9 13
15 2 8 9 14
16 23 13 9 10
17 23 14 9 10
18 1 13 9 14
19 6 9 10 11
20 4 9 10 12
21 24 1 10 9
22 25 11 10 12
23 26 1 10 11
24 27 1 10 12
25 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 10 8 9 10 11
20 8 8 9 10 12
21 31 8 9 10 1
22 11 13 9 10 11
23 9 13 9 10 12
24 32 13 9 10 1
25 11 14 9 10 11
26 9 14 9 10 12
27 32 14 9 10 1
28 6 9 10 12 15
29 7 11 10 12 15
30 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

795
examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data Normal file
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@ -0,0 +1,795 @@
this is LAMMPS data file containing two nylon monomers
44 atoms
11 atom types
42 bonds
15 bond types
74 angles
29 angle types
100 dihedrals
36 dihedral types
44 impropers
13 improper types
5 extra bond per atom
15 extra angle per atom
15 extra dihedral per atom
25 extra improper per atom
25 extra special per atom
-25 25 xlo xhi
-25 25 ylo yhi
-25 25 zlo zhi
Masses
1 12.0112
2 12.0112
3 15.9994
4 1.00797
5 1.00797
6 15.9994
7 14.0067
8 1.00797
9 14.0067
10 1.00797
11 15.9994
Pair Coeffs # lj/class2/coul/cut
1 0.054 4.01
2 0.12 3.81
3 0.24 3.535
4 0.02 2.7
5 0.013 1.098
6 0.267 3.3
7 0.065 4.07
8 0.013 1.098
9 0.106 4.07
10 0.013 1.098
11 0.26 3.61
Bond Coeffs # class2
1 1.101 345 -691.89 844.6
2 1.53 299.67 -501.77 679.81
3 1.3649 368.731 -832.478 1274.02
4 1.5202 253.707 -423.037 396.9
5 1.202 851.14 -1918.49 2160.77
6 0.965 532.506 -1282.9 2004.77
7 1.53 299.67 -501.77 679.81
8 1.101 345 -691.89 844.6
9 1.457 365.805 -699.637 998.484
10 1.006 466.74 -1073.6 1251.11
11 1.452 327.166 -547.899 526.5
12 1.01 462.75 -1053.63 1545.76
13 1.416 359.159 -558.473 1146.38
14 1.457 365.805 -699.637 998.484
15 0.97 563.28 -1428.22 1902.12
Angle Coeffs # class2
1 107.66 39.641 -12.921 -2.4318
2 110.77 41.453 -10.604 5.129
3 112.67 39.516 -7.443 -9.5583
4 123.145 55.5431 -17.2123 0.1348
5 118.986 98.6813 -22.2485 10.3673
6 123.145 55.5431 -17.2123 0.1348
7 111.254 53.5303 -11.8454 -11.5405
8 108.53 51.9747 -9.4851 -10.9985
9 107.734 40.6099 -28.8121 0
10 110.77 41.453 -10.604 5.129
11 112.67 39.516 -7.443 -9.5583
12 107.66 39.641 -12.921 -2.4318
13 111.91 60.7147 -13.3366 -13.0785
14 110.62 51.3137 -6.7198 -2.6003
15 110.954 50.8652 -4.4522 -10.0298
16 107.067 45.252 -7.5558 -9.512
17 113.868 45.9271 -20.0824 0
18 111.037 31.8958 -6.6942 -6.837
19 116.94 37.5749 -8.6676 0
20 117.961 37.4964 -8.1837 0
21 114.302 42.6589 -10.5464 -9.3243
22 108.937 57.401 2.9374 0
23 107.734 40.6099 -28.8121 0
24 116.926 39.4193 -10.9945 -8.7733
25 118.986 98.6813 -22.2485 10.3673
26 125.542 92.572 -34.48 -11.1871
27 0 0 0 0
28 111.91 60.7147 -13.3366 -13.0785
29 103.7 49.84 -11.6 -8
BondBond Coeffs
1 5.3316 1.101 1.101
2 3.3872 1.53 1.101
3 0 1.53 1.53
4 0 1.5202 1.3649
5 0 1.3649 1.202
6 46.0685 1.5202 1.202
7 0 1.3649 0.965
8 5.4199 1.53 1.5202
9 0.7115 1.5202 1.101
10 3.3872 1.53 1.101
11 0 1.53 1.53
12 5.3316 1.101 1.101
13 4.6217 1.53 1.457
14 12.426 1.457 1.101
15 -6.4168 1.457 1.006
16 -1.8749 1.006 1.006
17 -3.471 1.452 1.01
18 12.1186 1.452 1.416
19 -0.5655 1.01 1.01
20 -4.3126 1.01 1.416
21 3.5446 1.452 1.53
22 15.2994 1.452 1.101
23 0.7115 1.101 1.5202
24 0 1.416 1.5202
25 0 1.202 1.3649
26 138.495 1.416 1.202
27 0 1.416 1.3649
28 4.6217 1.457 1.53
29 -9.5 0.97 0.97
BondAngle Coeffs
1 18.103 18.103 1.101 1.101
2 20.754 11.421 1.53 1.101
3 8.016 8.016 1.53 1.53
4 0 0 1.5202 1.3649
5 0 0 1.3649 1.202
6 34.9982 37.1298 1.5202 1.202
7 0 0 1.3649 0.965
8 18.1678 15.8758 1.53 1.5202
9 12.4632 9.1765 1.5202 1.101
10 20.754 11.421 1.53 1.101
11 8.016 8.016 1.53 1.53
12 18.103 18.103 1.101 1.101
13 6.0876 16.5702 1.53 1.457
14 42.4332 13.4582 1.457 1.101
15 31.8096 20.5799 1.457 1.006
16 28.0322 28.0322 1.006 1.006
17 11.8828 5.9339 1.452 1.01
18 3.7812 14.8633 1.452 1.416
19 19.8125 19.8125 1.01 1.01
20 10.8422 29.5743 1.01 1.416
21 4.6031 -5.479 1.452 1.53
22 34.8907 10.6917 1.452 1.101
23 9.1765 12.4632 1.101 1.5202
24 0 0 1.416 1.5202
25 0 0 1.202 1.3649
26 62.7124 52.4045 1.416 1.202
27 0 0 1.416 1.3649
28 16.5702 6.0876 1.457 1.53
29 22.35 22.35 0.97 0.97
Dihedral Coeffs # class2
1 -0.0228 0 0.028 0 -0.1863 0
2 -0.1432 0 0.0617 0 -0.1083 0
3 0.0972 0 0.0722 0 -0.2581 0
4 0 0 0.0316 0 -0.1681 0
5 0 0 0.0514 0 -0.143 0
6 0 0 0 0 0 0
7 -2.7332 0 2.9646 0 -0.0155 0
8 0 0 0 0 0 0
9 0 0 0 0 0 0
10 0.0442 0 0.0292 0 0.0562 0
11 -0.1804 0 0.0012 0 0.0371 0
12 -0.2428 0 0.4065 0 -0.3079 0
13 -0.1432 0 0.0617 0 -0.1083 0
14 0.1764 0 0.1766 0 -0.5206 0
15 0 0 0.0316 0 -0.1681 0
16 0 0 0.0514 0 -0.143 0
17 -1.1506 0 -0.6344 0 -0.1845 0
18 -0.5187 0 -0.4837 0 -0.1692 0
19 -0.0483 0 -0.0077 0 -0.0014 0
20 -0.0148 0 -0.0791 0 -0.0148 0
21 0.0143 0 -0.0132 0 0.0091 0
22 0.0219 0 -0.026 0 0.0714 0
23 -0.7532 0 2.7392 0 0.0907 0
24 0.8297 0 3.7234 0 -0.0495 0
25 0 0 0 0 0 0
26 0 0 0 0 0 0
27 -1.6938 0 2.7386 0 -0.336 0
28 0 0 0 0 0 0
29 0.0972 0 0.0722 0 -0.2581 0
30 -0.0228 0 0.028 0 -0.1863 0
31 0.1693 0 -0.009 0 -0.0687 0
32 0.1693 0 -0.009 0 -0.0687 0
33 0 0 0 0 0 0
34 -1.1506 0 -0.6344 0 -0.1845 0
35 -0.5187 0 -0.4837 0 -0.1692 0
36 0.1764 0 0.1766 0 -0.5206 0
AngleAngleTorsion Coeffs
1 -5.3624 108.53 110.77
2 -12.564 110.77 110.77
3 -0.3801 112.67 108.53
4 -16.164 112.67 110.77
5 -22.045 112.67 112.67
6 0 0 111.254
7 0 118.985 111.254
8 0 108.53 0
9 0 107.734 0
10 -8.019 108.53 123.145
11 -15.3496 107.734 123.145
12 -15.7572 111.91 110.77
13 -12.564 110.77 110.77
14 -27.3953 112.67 111.91
15 -16.164 112.67 110.77
16 -22.045 112.67 112.67
17 -7.5499 111.91 110.954
18 -10.4258 110.62 110.954
19 -4.6337 113.868 114.302
20 -6.659 113.868 108.937
21 -7.4314 111.037 114.302
22 -8.1335 111.037 108.937
23 -6.5335 111.037 116.926
24 -15.5547 111.037 125.542
25 0 111.037 0
26 -1.3234 117.961 116.926
27 -7.3186 117.961 125.542
28 0 117.961 0
29 -1.0631 114.302 112.67
30 -12.7974 114.302 110.77
31 -5.4514 108.53 116.926
32 -12.2417 107.734 116.926
33 0 0 111.254
34 -7.5499 110.954 111.91
35 -10.4258 110.954 110.62
36 -27.3953 111.91 112.67
EndBondTorsion Coeffs
1 -0.0204 0.3628 -0.4426 -0.0097 -0.0315 -0.0755 1.5202 1.101
2 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
3 0.0062 -0.0002 0.0036 0.0055 0.006 -0.0009 1.53 1.5202
4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
5 -0.0732 0 0 -0.0732 0 0 1.53 1.53
6 0 0 0 0 0 0 1.5202 0.965
7 0 0 0 0 0 0 1.202 0.965
8 0 0 0 0 0 0 1.53 1.3649
9 0 0 0 0 0 0 1.101 1.3649
10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202
11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202
12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101
13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
16 -0.0732 0 0 -0.0732 0 0 1.53 1.53
17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
25 0 0 0 0 0 0 1.452 1.3649
26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
28 0 0 0 0 0 0 1.01 1.3649
29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
33 0 0 0 0 0 0 1.416 0.965
34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53
MiddleBondTorsion Coeffs
1 -3.5039 1.2458 -0.761 1.53
2 -14.261 -0.5322 -0.4864 1.53
3 -1.5945 0.2267 -0.6911 1.53
4 -14.879 -3.6581 -0.3138 1.53
5 -17.787 -7.1877 0 1.53
6 0 0 0 1.3649
7 0 0 0 1.3649
8 0 0 0 1.5202
9 0 0 0 1.5202
10 0.3388 -0.1096 0.1219 1.5202
11 0.2359 0.9139 0.9594 1.5202
12 -10.4959 -0.7647 -0.0545 1.53
13 -14.261 -0.5322 -0.4864 1.53
14 -15.4174 -7.3055 -1.0749 1.53
15 -14.879 -3.6581 -0.3138 1.53
16 -17.787 -7.1877 0 1.53
17 -2.2208 0.5479 -0.3527 1.457
18 -3.4611 1.6996 -0.6007 1.457
19 -3.5406 -3.3866 0.0352 1.452
20 -1.1752 2.8058 0.8083 1.452
21 -3.9501 -0.4002 -0.6798 1.452
22 -0.6899 -2.2646 1.1579 1.452
23 0 0 0 1.416
24 -8.8301 14.3079 -1.7716 1.416
25 0 0 0 1.416
26 0 0 0 1.416
27 -0.9084 6.1447 -0.4852 1.416
28 0 0 0 1.416
29 -4.2324 -3.3023 -1.3244 1.53
30 -4.1028 -0.5941 -0.047 1.53
31 0 0 0 1.5202
32 0 0 0 1.5202
33 0 0 0 1.3649
34 -2.2208 0.5479 -0.3527 1.457
35 -3.4611 1.6996 -0.6007 1.457
36 -15.4174 -7.3055 -1.0749 1.53
BondBond13 Coeffs
1 0 1.5202 1.101
2 0 1.101 1.101
3 0 1.53 1.5202
4 0 1.53 1.101
5 0 1.53 1.53
6 0 1.5202 0.965
7 0 1.202 0.965
8 0 1.53 1.3649
9 0 1.101 1.3649
10 0 1.53 1.202
11 0 1.101 1.202
12 0 1.457 1.101
13 0 1.101 1.101
14 0 1.53 1.457
15 0 1.53 1.101
16 0 1.53 1.53
17 0 1.53 1.006
18 0 1.101 1.006
19 0 1.01 1.53
20 0 1.01 1.101
21 0 1.416 1.53
22 0 1.416 1.101
23 0 1.452 1.5202
24 0 1.452 1.202
25 0 1.452 1.3649
26 0 1.01 1.5202
27 0 1.01 1.202
28 0 1.01 1.3649
29 0 1.452 1.53
30 0 1.452 1.101
31 0 1.53 1.416
32 0 1.101 1.416
33 0 1.416 0.965
34 0 1.006 1.53
35 0 1.006 1.101
36 0 1.457 1.53
AngleTorsion Coeffs
1 -0.7466 -0.9448 -0.6321 0.0162 1.4211 -1.4092 108.53 110.77
2 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
3 -0.2607 0.3203 -0.2283 0.0515 -0.0674 -0.0474 112.67 108.53
4 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
5 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
6 0 0 0 0 0 0 0 111.254
7 0 0 0 0 0 0 118.985 111.254
8 0 0 0 0 0 0 108.53 0
9 0 0 0 0 0 0 107.734 0
10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145
11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145
12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77
13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
25 0 0 0 0 0 0 111.037 0
26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
28 0 0 0 0 0 0 117.961 0
29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
33 0 0 0 0 0 0 0 111.254
34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
Improper Coeffs # class2
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 24.3329 0
AngleAngle Coeffs
1 0 0 0 0 118.985 123.145
2 0.2738 -0.4825 0.2738 110.77 107.66 110.77
3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
4 2.0403 -1.8202 1.0827 108.53 107.734 110.77
5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734
6 0 0 0 110.954 107.067 110.954
7 0.2738 -0.4825 0.2738 110.77 107.66 110.77
8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
9 -2.5301 0.5381 2.4286 111.91 110.62 110.77
10 2.4321 -3.5496 2.4321 110.62 107.66 110.62
11 0 0 0 123.145 118.985 0
12 0 0 0 113.868 117.961 111.037
13 0 0 0 116.926 123.145 125.542
Atoms # full
1 1 1 0.0000000000000000e+00 12.288168 0.738732 4.374280 0 0 0
2 1 2 2.9999999999999999e-01 13.959928 -0.883144 5.090597 0 0 0
3 1 3 0.0000000000000000e+00 14.411288 -1.994419 5.682160 0 0 0
4 1 4 0.0000000000000000e+00 12.881083 0.872503 3.506176 0 0 0
5 1 4 0.0000000000000000e+00 11.232775 0.801641 3.998777 0 0 0
6 1 5 0.0000000000000000e+00 13.704366 -2.470396 6.130105 0 0 0
7 1 1 0.0000000000000000e+00 12.489752 -0.793693 4.710639 0 0 0
8 1 1 0.0000000000000000e+00 12.455071 1.866388 5.385870 0 0 0
9 1 1 0.0000000000000000e+00 11.248961 1.901849 6.347664 0 0 0
10 1 2 2.9999999999999999e-01 10.005971 2.466710 5.772840 -1 1 0
11 1 6 0.0000000000000000e+00 14.795360 -0.034436 4.807367 0 0 0
12 1 6 0.0000000000000000e+00 9.115239 1.654547 5.617002 -1 0 0
13 1 3 0.0000000000000000e+00 9.745096 3.807654 5.573585 -1 1 0
14 1 4 0.0000000000000000e+00 12.248215 -1.371492 3.808598 0 0 0
15 1 4 0.0000000000000000e+00 11.715755 -1.036825 5.500449 0 0 0
16 1 4 0.0000000000000000e+00 12.559724 2.807687 4.858452 0 1 0
17 1 4 0.0000000000000000e+00 13.299968 1.616570 6.123781 0 0 0
18 1 4 0.0000000000000000e+00 11.650505 2.330454 7.282410 0 1 0
19 1 4 0.0000000000000000e+00 10.888420 0.913219 6.637162 -1 0 0
20 1 5 0.0000000000000000e+00 10.550073 4.294209 5.758192 -1 1 0
21 2 1 0.0000000000000000e+00 5.851425 1.929552 6.038335 0 0 0
22 2 1 0.0000000000000000e+00 6.741509 3.160751 6.233074 0 0 0
23 2 7 -2.9999999999999999e-01 7.957761 3.121780 5.252257 1 0 0
24 2 7 -2.9999999999999999e-01 2.599653 -2.258940 5.985863 0 -1 0
25 2 1 0.0000000000000000e+00 3.834337 -1.907078 5.441528 0 -1 0
26 2 1 0.0000000000000000e+00 4.810793 -1.083699 6.310184 0 -1 0
27 2 4 0.0000000000000000e+00 6.505912 1.182799 5.449104 0 0 0
28 2 4 0.0000000000000000e+00 5.156429 2.256468 5.348423 0 0 0
29 2 4 0.0000000000000000e+00 7.232782 3.178785 7.181911 0 0 0
30 2 4 0.0000000000000000e+00 6.251671 4.103621 6.222913 0 0 0
31 2 8 0.0000000000000000e+00 8.249909 4.070668 4.881297 1 0 0
32 2 8 0.0000000000000000e+00 7.813025 2.623184 4.400744 1 0 0
33 2 8 0.0000000000000000e+00 2.626695 -2.857547 6.817247 0 -1 0
34 2 8 0.0000000000000000e+00 1.955281 -2.684319 5.328460 0 -1 0
35 2 4 0.0000000000000000e+00 3.637708 -1.322842 4.469265 0 -1 0
36 2 4 0.0000000000000000e+00 4.415570 -2.739689 4.997336 0 -1 0
37 2 4 0.0000000000000000e+00 5.710714 -1.010014 5.642798 0 -1 0
38 2 4 0.0000000000000000e+00 5.103831 -1.696423 7.160345 0 -1 0
39 2 1 0.0000000000000000e+00 5.270763 1.286629 7.308822 0 0 0
40 2 4 0.0000000000000000e+00 4.834381 2.168531 7.931687 0 0 1
41 2 4 0.0000000000000000e+00 6.118354 0.786724 7.794709 0 0 1
42 2 1 0.0000000000000000e+00 4.273849 0.167695 6.957862 0 -1 0
43 2 4 0.0000000000000000e+00 3.792544 -0.081782 7.904418 0 -1 1
44 2 4 0.0000000000000000e+00 3.527495 0.674238 6.348869 0 0 0
Velocities
1 -2.4626989626218821e-03 -1.5920230003311222e-03 -3.0621927786115238e-03
2 9.5082416704385837e-03 -6.9903166167507250e-03 1.3702671335945608e-02
3 2.3431518493187576e-03 -2.9261683108242173e-03 1.4269399726982105e-03
4 -1.8184451408256214e-02 3.1103803691687960e-02 -1.3358827768357973e-02
5 2.6084132471017967e-02 -1.0819576493517332e-02 3.0403384454794881e-02
6 -4.7312115958218744e-03 -1.9111462399478338e-02 -3.6793354156497558e-02
7 -7.5068797595949869e-03 6.5661422055962489e-03 1.3226575122695422e-03
8 3.3807881380161281e-03 3.0458732663557089e-03 2.2368826795446284e-03
9 -3.1113905793879316e-03 8.2908867720754773e-03 -1.7561238039496530e-03
10 2.4685206571693056e-03 1.3194776209841030e-03 -2.8041877032800441e-03
11 -3.4945605770565296e-03 3.2323777135621814e-03 1.6223017668450866e-03
12 -6.1153483612847778e-03 -5.1534857074262185e-03 1.7735747357354274e-03
13 2.1384296781859011e-04 -4.5398902942729667e-03 6.1649769894413760e-03
14 2.5004619864373401e-03 -1.5709184283264888e-03 2.0837548254667757e-02
15 6.0547939205643532e-03 -1.2650704436910937e-02 -5.4430753266962190e-03
16 -1.0374605775698001e-02 9.1408658463889240e-03 -1.1306875858287088e-02
17 -1.2736499128987409e-02 -9.1726811852506501e-03 5.1136502685461254e-03
18 7.6741778607048112e-03 1.8629856635459279e-02 -1.1300096447670932e-02
19 -1.8616138775281121e-02 1.0848388547730185e-03 -5.7118433687798576e-03
20 5.4137572241479059e-03 -1.4564578166395727e-02 -1.2618420441909540e-02
21 5.8473521452312256e-03 -4.0595286000332086e-03 -6.2517801580146415e-03
22 3.6402033824753104e-03 -1.4629540504663154e-03 -4.0030712318898046e-03
23 9.0266305019107689e-03 -2.7511425384659687e-03 4.5576402565437142e-03
24 -1.3102302415548614e-02 -4.7286703965305791e-03 -1.8966887841189517e-03
25 7.8621682621103171e-03 -4.2046313540949568e-03 9.6887957374751301e-04
26 -4.7380176438337968e-03 9.6090441940775827e-03 -8.7592431387039336e-03
27 5.4311658811632517e-03 2.0032224663495989e-02 -9.4952076489808503e-03
28 -2.9056381493904374e-03 3.3317109723156875e-03 1.6650350064426677e-02
29 -6.4569944033489122e-03 2.8423983541959541e-03 -2.6066912906505167e-02
30 -2.2173867823429387e-02 1.4628839880961319e-02 -2.3330833961402380e-02
31 9.1925713381983114e-03 -2.5697556639281928e-03 -1.2822203161488303e-02
32 -8.3206975051927905e-03 -2.2538429924858707e-03 7.7620244118580314e-03
33 1.9920685674825727e-02 5.0317764848494097e-03 -2.1106672824976403e-02
34 1.4118463330250982e-02 1.7455545466840316e-02 -1.2482101375598437e-02
35 -6.1116505640437966e-03 1.3353021777303568e-02 -2.5492434283827668e-02
36 9.1001521565859649e-03 5.5737774505222404e-03 1.4573768978939985e-02
37 1.6523593470528035e-03 -2.2107518020000917e-02 2.0311423445130115e-02
38 -1.0346275393471860e-02 1.6055856586351790e-02 5.5489127019262424e-03
39 -3.2054811383248638e-03 1.6779208962376315e-03 2.9390509537535661e-03
40 1.9649219364916443e-02 4.0815776523222859e-03 -9.8422441166041274e-03
41 5.6961697588160361e-04 7.1361132234741477e-04 4.6335764220256257e-03
42 2.2221300208006252e-03 3.6217319632558197e-03 -6.3299398503455151e-03
43 2.5710172734841170e-03 8.0029179814482924e-03 1.9992986928468189e-02
44 -6.0827581822674656e-03 -1.1834273655641976e-02 2.0526923045885208e-02
Bonds
1 1 1 5
2 1 1 4
3 2 1 7
4 2 1 8
5 3 2 3
6 5 2 11
7 6 3 6
8 4 7 2
9 1 7 14
10 1 7 15
11 2 8 9
12 1 8 16
13 1 8 17
14 4 9 10
15 1 9 18
16 1 9 19
17 5 10 12
18 3 10 13
19 6 13 20
20 7 21 22
21 8 21 27
22 8 21 28
23 7 21 39
24 9 22 23
25 8 22 29
26 8 22 30
27 10 23 31
28 10 23 32
29 10 24 33
30 10 24 34
31 9 25 24
32 7 25 26
33 8 25 35
34 8 25 36
35 8 26 37
36 8 26 38
37 7 26 42
38 8 39 40
39 8 39 41
40 7 39 42
41 8 42 43
42 8 42 44
Angles
1 1 5 1 4
2 2 7 1 5
3 2 8 1 5
4 2 7 1 4
5 2 8 1 4
6 3 7 1 8
7 4 7 2 3
8 5 3 2 11
9 6 7 2 11
10 7 2 3 6
11 8 1 7 2
12 2 1 7 14
13 2 1 7 15
14 9 2 7 14
15 9 2 7 15
16 1 14 7 15
17 3 1 8 9
18 2 1 8 16
19 2 1 8 17
20 2 9 8 16
21 2 9 8 17
22 1 16 8 17
23 8 8 9 10
24 2 8 9 18
25 2 8 9 19
26 9 10 9 18
27 9 10 9 19
28 1 18 9 19
29 6 9 10 12
30 4 9 10 13
31 5 13 10 12
32 7 10 13 20
33 10 22 21 27
34 10 22 21 28
35 11 22 21 39
36 12 27 21 28
37 10 39 21 27
38 10 39 21 28
39 13 21 22 23
40 10 21 22 29
41 10 21 22 30
42 14 23 22 29
43 14 23 22 30
44 12 29 22 30
45 15 22 23 31
46 15 22 23 32
47 16 31 23 32
48 15 25 24 33
49 15 25 24 34
50 16 33 24 34
51 13 26 25 24
52 14 24 25 35
53 14 24 25 36
54 10 26 25 35
55 10 26 25 36
56 12 35 25 36
57 10 25 26 37
58 10 25 26 38
59 11 25 26 42
60 12 37 26 38
61 10 42 26 37
62 10 42 26 38
63 10 21 39 40
64 10 21 39 41
65 11 21 39 42
66 12 40 39 41
67 10 42 39 40
68 10 42 39 41
69 11 26 42 39
70 10 26 42 43
71 10 26 42 44
72 10 39 42 43
73 10 39 42 44
74 12 43 42 44
Dihedrals
1 2 5 1 7 14
2 2 5 1 7 15
3 2 4 1 7 14
4 2 4 1 7 15
5 3 8 1 7 2
6 4 8 1 7 14
7 4 8 1 7 15
8 2 5 1 8 16
9 2 5 1 8 17
10 2 4 1 8 16
11 2 4 1 8 17
12 5 7 1 8 9
13 4 7 1 8 16
14 4 7 1 8 17
15 6 7 2 3 6
16 7 11 2 3 6
17 1 2 7 1 5
18 1 2 7 1 4
19 8 1 7 2 3
20 9 14 7 2 3
21 9 15 7 2 3
22 10 1 7 2 11
23 11 14 7 2 11
24 11 15 7 2 11
25 4 9 8 1 5
26 4 9 8 1 4
27 3 1 8 9 10
28 4 1 8 9 18
29 4 1 8 9 19
30 2 16 8 9 18
31 2 16 8 9 19
32 2 17 8 9 18
33 2 17 8 9 19
34 1 10 9 8 16
35 1 10 9 8 17
36 10 8 9 10 12
37 8 8 9 10 13
38 11 18 9 10 12
39 9 18 9 10 13
40 11 19 9 10 12
41 9 19 9 10 13
42 6 9 10 13 20
43 7 12 10 13 20
44 13 27 21 22 29
45 13 27 21 22 30
46 13 28 21 22 29
47 13 28 21 22 30
48 14 39 21 22 23
49 15 39 21 22 29
50 15 39 21 22 30
51 15 22 21 39 40
52 15 22 21 39 41
53 16 22 21 39 42
54 13 27 21 39 40
55 13 27 21 39 41
56 13 28 21 39 40
57 13 28 21 39 41
58 12 23 22 21 27
59 12 23 22 21 28
60 17 21 22 23 31
61 17 21 22 23 32
62 18 29 22 23 31
63 18 29 22 23 32
64 18 30 22 23 31
65 18 30 22 23 32
66 17 26 25 24 33
67 18 35 25 24 33
68 18 36 25 24 33
69 17 26 25 24 34
70 18 35 25 24 34
71 18 36 25 24 34
72 12 24 25 26 37
73 12 24 25 26 38
74 13 35 25 26 37
75 13 35 25 26 38
76 13 36 25 26 37
77 13 36 25 26 38
78 14 42 26 25 24
79 15 42 26 25 35
80 15 42 26 25 36
81 16 25 26 42 39
82 15 25 26 42 43
83 15 25 26 42 44
84 13 37 26 42 43
85 13 37 26 42 44
86 13 38 26 42 43
87 13 38 26 42 44
88 15 42 39 21 27
89 15 42 39 21 28
90 16 21 39 42 26
91 15 21 39 42 43
92 15 21 39 42 44
93 13 40 39 42 43
94 13 40 39 42 44
95 13 41 39 42 43
96 13 41 39 42 44
97 15 39 42 26 37
98 15 39 42 26 38
99 15 26 42 39 40
100 15 26 42 39 41
Impropers
1 2 7 1 4 5
2 2 8 1 4 5
3 3 7 1 8 5
4 3 7 1 8 4
5 1 7 2 3 11
6 4 1 7 2 14
7 4 1 7 2 15
8 2 1 7 14 15
9 5 2 7 14 15
10 3 1 8 9 16
11 3 1 8 9 17
12 2 1 8 16 17
13 2 9 8 16 17
14 4 8 9 10 18
15 4 8 9 10 19
16 2 8 9 18 19
17 5 10 9 18 19
18 1 9 10 13 12
19 7 22 21 27 28
20 8 22 21 39 27
21 8 22 21 39 28
22 7 39 21 28 27
23 9 21 22 23 29
24 9 21 22 23 30
25 7 21 22 29 30
26 10 23 22 29 30
27 6 22 23 31 32
28 6 25 24 33 34
29 9 26 25 24 35
30 9 26 25 24 36
31 10 24 25 35 36
32 7 26 25 35 36
33 7 25 26 37 38
34 8 25 26 42 37
35 8 25 26 42 38
36 7 42 26 38 37
37 7 21 39 40 41
38 8 21 39 42 40
39 8 21 39 42 41
40 7 42 39 41 40
41 8 26 42 39 43
42 8 26 42 39 44
43 7 26 42 43 44
44 7 39 42 43 44

0
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0
examples/rigid/in.rigid-atomvar → examples/rigid/in.rigid.atomvar
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83
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# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
clump6 clump7 clump8 clump9
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000

81
examples/rigid/in.rigid.nve Normal file
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@ -0,0 +1,81 @@
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000

83
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@ -0,0 +1,83 @@
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
group clump2 id <> 10 18
group clump3 id <> 19 27
group clump4 id <> 28 36
group clump5 id <> 37 45
group clump6 id <> 46 54
group clump7 id <> 55 63
group clump8 id <> 64 72
group clump9 id <> 73 81
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
clump6 clump7 clump8 clump9
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
# clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000

0
examples/rigid/in.rigid-property → examples/rigid/in.rigid.property
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338
examples/rigid/log.20Apr18.rigid.atomfile.g++.1 Normal file
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@ -0,0 +1,338 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.109 | 4.109 | 4.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550102 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms
Performance: 615179.112 tau/day, 71201.286 timesteps/s
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37
Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06
Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58
Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70
Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01
Other | | 0.006017 | | | 4.28
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
examples/rigid/log.20Apr18.rigid.atomfile.g++.4 Normal file
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@ -0,0 +1,338 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atomfile bodies.txt
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.08 | 4.174 | 4.455 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.135501 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms
Performance: 451214.099 tau/day, 52223.854 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91
Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27
Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59
Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38
Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82
Other | | 0.009611 | | | 5.02
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.984 | 3.984 | 3.984 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550102 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms
Performance: 621477.474 tau/day, 71930.263 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 | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40
Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59
Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57
Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73
Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24
Other | | 0.006207 | | | 4.46
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
fix 1 all rigid custom v_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.955 | 4.049 | 4.33 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.135501 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms
Performance: 426175.966 tau/day, 49325.922 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83
Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92
Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37
Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32
Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76
Other | | 0.009733 | | | 4.80
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

337
examples/rigid/log.20Apr18.rigid.early.g++.1 Normal file
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550102 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms
Performance: 607236.588 tau/day, 70282.013 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 | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52
Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64
Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12
Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82
Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65
Other | | 0.006064 | | | 4.26
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

337
examples/rigid/log.20Apr18.rigid.early.g++.4 Normal file
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@ -0,0 +1,337 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.135501 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms
Performance: 505560.431 tau/day, 58513.939 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22
Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05
Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40
Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42
Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46
Other | | 0.009313 | | | 5.45
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

62
examples/rigid/log.5Oct16.rigid.g++.4 → examples/rigid/log.20Apr18.rigid.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 3.62803 Mbytes
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550102 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms
Performance: 509796.561 tau/day, 59004.232 timesteps/s
98.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 554075.151 tau/day, 64129.068 timesteps/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
Other | | 0.006244 | | | 3.68
Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34
Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86
Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08
Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69
Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75
Other | | 0.006683 | | | 4.29
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0

72
examples/rigid/log.5Oct16.rigid.g++.1 → examples/rigid/log.20Apr18.rigid.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 3.65531 Mbytes
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.135501 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms
Performance: 687503.421 tau/day, 79572.155 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 444142.918 tau/day, 51405.430 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
Other | | 0.004176 | | | 3.32
Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97
Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18
Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24
Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43
Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24
Other | | 0.009634 | | | 4.95
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0

337
examples/rigid/log.20Apr18.rigid.nve.early.g++.1 Normal file
View File

@ -0,0 +1,337 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521421 0 5269.4761 12.385777
4800 16735.057 1.0347219 0 5269.4786 12.43543
4850 16735.441 0.92650928 0 5269.4913 12.418653
4900 16723.839 4.5908971 0 5269.5033 13.410103
4950 16738.531 -0.021537669 0 5269.5159 13.089982
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
5300 16738.456 -0.0064376397 0 5269.5075 13.090026
5350 16738.479 -0.020383842 0 5269.5007 13.089898
5400 16735.845 0.79889481 0 5269.4909 13.136244
5450 16735.558 0.87619898 0 5269.4778 12.324482
5500 16711.494 8.47243 0 5269.4984 12.65658
5550 16454.525 89.074845 0 5269.2031 16.996503
5600 16713.084 7.9801091 0 5269.5065 13.774971
5650 16738.676 -0.079987812 0 5269.5033 13.168292
5700 16446.281 91.866085 0 5269.399 23.764658
5750 16738.549 -0.039869082 0 5269.5034 13.378117
5800 16738.487 -0.014994464 0 5269.5086 13.378394
5850 16738.466 -0.0051267378 0 5269.512 13.378555
5900 16738.462 -0.0043689966 0 5269.5113 13.378568
5950 16738.528 -0.032727396 0 5269.5039 13.378192
6000 16702.774 10.969422 0 5269.2502 13.788847
6050 16682.271 17.483217 0 5269.3092 13.353098
6100 16738.508 -0.028838289 0 5269.5016 12.521077
6150 16738.425 -0.0067595568 0 5269.4974 12.521216
6200 16738.401 -0.0011499904 0 5269.4955 12.521247
6250 16738.455 0 0 5269.5136 12.521403
6300 16738.523 0 0 5269.5352 12.521573
6350 16738.503 0 0 5269.5287 12.521525
6400 16738.427 0 0 5269.5047 12.521337
6450 16738.399 0 0 5269.496 12.521268
6500 16738.425 0 0 5269.5042 12.521331
6550 16738.441 0 0 5269.5093 12.521372
6600 16738.42 0 0 5269.5025 12.521319
6650 16738.398 0 0 5269.4957 12.521266
6700 16738.435 0 0 5269.5074 12.521355
6750 16738.505 0 0 5269.5293 12.521527
6800 16738.508 0 0 5269.5303 12.521536
6850 16738.446 0 0 5269.5108 12.521384
6900 16738.414 0 0 5269.5009 12.521306
6950 16738.432 0 0 5269.5063 12.521348
7000 16738.444 0 0 5269.5102 12.521378
7050 16738.421 0 0 5269.5029 12.521322
7100 16738.393 0 0 5269.4941 12.521253
7150 16738.419 0 0 5269.5022 12.521315
7200 16738.489 0 0 5269.5244 12.521489
7250 16738.505 0 0 5269.5293 12.521528
7300 16738.443 0 0 5269.5098 12.521376
7350 16738.404 0 0 5269.4976 12.521281
7400 16738.43 0 0 5269.5058 12.521343
7450 16738.461 0 0 5269.5156 12.521421
7500 16738.447 0 0 5269.5109 12.521385
7550 16738.407 0 0 5269.4986 12.521288
7600 16738.412 0 0 5269.5002 12.5213
7650 16738.478 0 0 5269.5208 12.52146
7700 16738.51 0 0 5269.5309 12.521541
7750 16738.454 0 0 5269.5135 12.521405
7800 16738.398 0 0 5269.4958 12.521267
7850 16738.407 -0.0002118068 0 5269.4982 12.521283
7900 16738.441 -0.00021679441 0 5269.509 12.521366
7950 16738.446 -0.00023847865 0 5269.5107 12.52138
8000 16738.423 0 0 5269.5035 12.521326
8050 16738.423 0 0 5269.5034 12.521325
8100 16738.478 -0.00069624411 0 5269.52 12.521447
8150 16738.523 -0.0040058094 0 5269.531 12.521494
8200 16738.486 -0.0092298399 0 5269.5142 12.521327
8250 16738.458 -0.023189572 0 5269.4914 12.521008
8300 16738.513 -0.045847775 0 5269.4861 12.520773
8350 16723.734 4.5722877 0 5269.4516 12.849562
8400 16738.466 -0.020202622 0 5269.497 12.835807
8450 16738.437 -0.012822209 0 5269.4952 12.829975
8500 16738.408 -0.001683355 0 5269.4972 12.8301
8550 16738.464 -0.00097382251 0 5269.5155 12.830254
8600 16738.669 -0.050581166 0 5269.5304 12.829973
8650 15918.256 250.07455 0 5261.3774 24.539208
8700 16738.446 0.00084613367 0 5269.5116 10.591358
8750 16738.472 -0.010145611 0 5269.5089 10.590277
8800 16738.468 0 0 5269.5176 10.590497
8850 16738.508 0 0 5269.5303 10.590596
8900 16738.509 0 0 5269.5306 10.590599
8950 16738.496 0 0 5269.5266 10.590568
9000 16738.477 0 0 5269.5204 10.59052
9050 16738.455 0 0 5269.5135 10.590465
9100 16738.477 0 0 5269.5205 10.590519
9150 16738.512 0 0 5269.5315 10.590606
9200 16738.502 0 0 5269.5285 10.590583
9250 16738.493 0 0 5269.5254 10.590559
9300 16738.482 0 0 5269.522 10.590532
9350 16738.46 0 0 5269.5151 10.590478
9400 16738.48 0 0 5269.5216 10.590528
9450 16738.509 0 0 5269.5306 10.590599
9500 16738.49 0 0 5269.5247 10.590554
9550 16738.484 0 0 5269.5226 10.590536
9600 16738.483 0 0 5269.5223 10.590534
9650 16738.464 0 0 5269.5165 10.590489
9700 16738.484 0 0 5269.5228 10.590537
9750 16738.507 0 0 5269.53 10.590595
9800 16738.482 0 0 5269.522 10.590532
9850 16738.478 0 0 5269.5207 10.590521
9900 16738.487 -0.00030979882 0 5269.5233 10.590538
9950 16738.476 -0.00095967357 0 5269.5193 10.590496
10000 16738.494 -0.00062714625 0 5269.5253 10.590548
Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms
Performance: 519549.516 tau/day, 60133.046 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 | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03
Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17
Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19
Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60
Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39
Other | | 0.00603 | | | 3.63
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 49 ave 49 max 49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
fix_modify 1 bodyforces early
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521424 0 5269.4761 12.385777
4800 16735.057 1.0347218 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908973 0 5269.5033 13.410103
4950 16738.531 -0.021537669 0 5269.5159 13.089982
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
5300 16738.456 -0.0064376396 0 5269.5075 13.090026
5350 16738.479 -0.020383843 0 5269.5007 13.089898
5400 16735.845 0.79889489 0 5269.4909 13.136244
5450 16735.558 0.87619907 0 5269.4778 12.324482
5500 16711.494 8.4724273 0 5269.4984 12.656579
5550 16454.525 89.074821 0 5269.2031 16.996502
5600 16713.084 7.9801107 0 5269.5065 13.774972
5650 16738.676 -0.079987805 0 5269.5033 13.168292
5700 16446.281 91.866085 0 5269.399 23.764659
5750 16738.549 -0.039869082 0 5269.5034 13.378118
5800 16738.487 -0.014994465 0 5269.5086 13.378394
5850 16738.466 -0.0051267396 0 5269.512 13.378555
5900 16738.462 -0.004368998 0 5269.5113 13.378568
5950 16738.528 -0.032727397 0 5269.5039 13.378192
6000 16702.774 10.969422 0 5269.2502 13.788847
6050 16682.271 17.483223 0 5269.3092 13.353098
6100 16738.508 -0.028838294 0 5269.5016 12.521077
6150 16738.425 -0.0067595586 0 5269.4974 12.521216
6200 16738.401 -0.0011499906 0 5269.4955 12.521248
6250 16738.455 0 0 5269.5136 12.521404
6300 16738.523 0 0 5269.5352 12.521573
6350 16738.503 0 0 5269.5287 12.521525
6400 16738.427 0 0 5269.5047 12.521337
6450 16738.399 0 0 5269.496 12.521268
6500 16738.425 0 0 5269.5042 12.521331
6550 16738.441 0 0 5269.5093 12.521372
6600 16738.42 0 0 5269.5025 12.521319
6650 16738.398 0 0 5269.4957 12.521266
6700 16738.435 0 0 5269.5074 12.521355
6750 16738.505 0 0 5269.5293 12.521527
6800 16738.508 0 0 5269.5303 12.521536
6850 16738.446 0 0 5269.5108 12.521384
6900 16738.414 0 0 5269.5009 12.521306
6950 16738.432 0 0 5269.5063 12.521348
7000 16738.444 0 0 5269.5102 12.521379
7050 16738.421 0 0 5269.5029 12.521322
7100 16738.393 0 0 5269.4941 12.521253
7150 16738.419 0 0 5269.5022 12.521315
7200 16738.489 0 0 5269.5244 12.521489
7250 16738.505 0 0 5269.5293 12.521528
7300 16738.443 0 0 5269.5098 12.521377
7350 16738.404 0 0 5269.4976 12.521281
7400 16738.43 0 0 5269.5058 12.521344
7450 16738.461 0 0 5269.5156 12.521421
7500 16738.447 0 0 5269.5109 12.521385
7550 16738.407 0 0 5269.4986 12.521288
7600 16738.412 0 0 5269.5002 12.5213
7650 16738.478 0 0 5269.5208 12.521461
7700 16738.51 0 0 5269.5309 12.521541
7750 16738.454 0 0 5269.5135 12.521406
7800 16738.398 0 0 5269.4958 12.521267
7850 16738.407 -0.00021180715 0 5269.4982 12.521283
7900 16738.441 -0.0002167946 0 5269.509 12.521367
7950 16738.446 -0.0002384787 0 5269.5107 12.52138
8000 16738.423 0 0 5269.5035 12.521327
8050 16738.423 0 0 5269.5034 12.521325
8100 16738.478 -0.00069624484 0 5269.52 12.521448
8150 16738.523 -0.0040058183 0 5269.531 12.521494
8200 16738.486 -0.0092298512 0 5269.5142 12.521328
8250 16738.458 -0.023189661 0 5269.4914 12.521008
8300 16738.513 -0.045847765 0 5269.4861 12.520773
8350 16723.735 4.5720344 0 5269.4516 12.849543
8400 16738.466 -0.02019859 0 5269.497 12.835812
8450 16738.437 -0.012822198 0 5269.4952 12.829979
8500 16738.408 -0.0016833646 0 5269.4972 12.830104
8550 16738.464 -0.00097382606 0 5269.5155 12.830258
8600 16738.669 -0.050581176 0 5269.5304 12.829977
8650 15918.073 250.131 0 5261.3761 24.542327
8700 16738.446 0.00085039409 0 5269.5116 10.59114
8750 16738.472 -0.010146632 0 5269.5089 10.590059
8800 16738.468 0 0 5269.5176 10.590278
8850 16738.508 0 0 5269.5303 10.590378
8900 16738.509 0 0 5269.5306 10.590381
8950 16738.496 0 0 5269.5266 10.590349
9000 16738.477 0 0 5269.5204 10.590302
9050 16738.455 0 0 5269.5135 10.590247
9100 16738.477 0 0 5269.5205 10.590301
9150 16738.512 0 0 5269.5315 10.590388
9200 16738.502 0 0 5269.5285 10.590364
9250 16738.493 0 0 5269.5254 10.59034
9300 16738.482 0 0 5269.522 10.590314
9350 16738.46 0 0 5269.5151 10.59026
9400 16738.48 0 0 5269.5216 10.59031
9450 16738.509 0 0 5269.5306 10.590381
9500 16738.49 0 0 5269.5247 10.590335
9550 16738.484 0 0 5269.5226 10.590318
9600 16738.483 0 0 5269.5223 10.590316
9650 16738.464 0 0 5269.5165 10.590271
9700 16738.484 0 0 5269.5228 10.590319
9750 16738.507 0 0 5269.53 10.590376
9800 16738.482 0 0 5269.522 10.590314
9850 16738.478 0 0 5269.5207 10.590303
9900 16738.487 -0.00030979874 0 5269.5233 10.59032
9950 16738.476 -0.00095967134 0 5269.5192 10.590278
10000 16738.494 -0.00062714318 0 5269.5253 10.590329
Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms
Performance: 384323.005 tau/day, 44481.829 timesteps/s
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75
Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41
Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63
Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03
Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73
Other | | 0.01001 | | | 4.45
Nlocal: 20.25 ave 34 max 9 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 38.5 ave 43 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0.75 ave 2 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521421 0 5269.4761 12.385777
4800 16735.057 1.0347219 0 5269.4786 12.43543
4850 16735.441 0.92650928 0 5269.4913 12.418653
4900 16723.839 4.5908971 0 5269.5033 13.410103
4950 16738.531 -0.021537669 0 5269.5159 13.089982
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
5300 16738.456 -0.0064376397 0 5269.5075 13.090026
5350 16738.479 -0.020383842 0 5269.5007 13.089898
5400 16735.845 0.79889481 0 5269.4909 13.136244
5450 16735.558 0.87619898 0 5269.4778 12.324482
5500 16711.494 8.47243 0 5269.4984 12.65658
5550 16454.525 89.074845 0 5269.2031 16.996503
5600 16713.084 7.9801091 0 5269.5065 13.774971
5650 16738.676 -0.079987812 0 5269.5033 13.168292
5700 16446.281 91.866085 0 5269.399 23.764658
5750 16738.549 -0.039869082 0 5269.5034 13.378117
5800 16738.487 -0.014994464 0 5269.5086 13.378394
5850 16738.466 -0.0051267378 0 5269.512 13.378555
5900 16738.462 -0.0043689966 0 5269.5113 13.378568
5950 16738.528 -0.032727396 0 5269.5039 13.378192
6000 16702.774 10.969422 0 5269.2502 13.788847
6050 16682.271 17.483217 0 5269.3092 13.353098
6100 16738.508 -0.028838289 0 5269.5016 12.521077
6150 16738.425 -0.0067595568 0 5269.4974 12.521216
6200 16738.401 -0.0011499904 0 5269.4955 12.521247
6250 16738.455 0 0 5269.5136 12.521403
6300 16738.523 0 0 5269.5352 12.521573
6350 16738.503 0 0 5269.5287 12.521525
6400 16738.427 0 0 5269.5047 12.521337
6450 16738.399 0 0 5269.496 12.521268
6500 16738.425 0 0 5269.5042 12.521331
6550 16738.441 0 0 5269.5093 12.521372
6600 16738.42 0 0 5269.5025 12.521319
6650 16738.398 0 0 5269.4957 12.521266
6700 16738.435 0 0 5269.5074 12.521355
6750 16738.505 0 0 5269.5293 12.521527
6800 16738.508 0 0 5269.5303 12.521536
6850 16738.446 0 0 5269.5108 12.521384
6900 16738.414 0 0 5269.5009 12.521306
6950 16738.432 0 0 5269.5063 12.521348
7000 16738.444 0 0 5269.5102 12.521378
7050 16738.421 0 0 5269.5029 12.521322
7100 16738.393 0 0 5269.4941 12.521253
7150 16738.419 0 0 5269.5022 12.521315
7200 16738.489 0 0 5269.5244 12.521489
7250 16738.505 0 0 5269.5293 12.521528
7300 16738.443 0 0 5269.5098 12.521376
7350 16738.404 0 0 5269.4976 12.521281
7400 16738.43 0 0 5269.5058 12.521343
7450 16738.461 0 0 5269.5156 12.521421
7500 16738.447 0 0 5269.5109 12.521385
7550 16738.407 0 0 5269.4986 12.521288
7600 16738.412 0 0 5269.5002 12.5213
7650 16738.478 0 0 5269.5208 12.52146
7700 16738.51 0 0 5269.5309 12.521541
7750 16738.454 0 0 5269.5135 12.521405
7800 16738.398 0 0 5269.4958 12.521267
7850 16738.407 -0.0002118068 0 5269.4982 12.521283
7900 16738.441 -0.00021679441 0 5269.509 12.521366
7950 16738.446 -0.00023847865 0 5269.5107 12.52138
8000 16738.423 0 0 5269.5035 12.521326
8050 16738.423 0 0 5269.5034 12.521325
8100 16738.478 -0.00069624411 0 5269.52 12.521447
8150 16738.523 -0.0040058094 0 5269.531 12.521494
8200 16738.486 -0.0092298399 0 5269.5142 12.521327
8250 16738.458 -0.023189572 0 5269.4914 12.521008
8300 16738.513 -0.045847775 0 5269.4861 12.520773
8350 16723.734 4.5722877 0 5269.4516 12.849562
8400 16738.466 -0.020202622 0 5269.497 12.835807
8450 16738.437 -0.012822209 0 5269.4952 12.829975
8500 16738.408 -0.001683355 0 5269.4972 12.8301
8550 16738.464 -0.00097382251 0 5269.5155 12.830254
8600 16738.669 -0.050581166 0 5269.5304 12.829973
8650 15918.256 250.07455 0 5261.3774 24.539208
8700 16738.446 0.00084613367 0 5269.5116 10.591358
8750 16738.472 -0.010145611 0 5269.5089 10.590277
8800 16738.468 0 0 5269.5176 10.590497
8850 16738.508 0 0 5269.5303 10.590596
8900 16738.509 0 0 5269.5306 10.590599
8950 16738.496 0 0 5269.5266 10.590568
9000 16738.477 0 0 5269.5204 10.59052
9050 16738.455 0 0 5269.5135 10.590465
9100 16738.477 0 0 5269.5205 10.590519
9150 16738.512 0 0 5269.5315 10.590606
9200 16738.502 0 0 5269.5285 10.590583
9250 16738.493 0 0 5269.5254 10.590559
9300 16738.482 0 0 5269.522 10.590532
9350 16738.46 0 0 5269.5151 10.590478
9400 16738.48 0 0 5269.5216 10.590528
9450 16738.509 0 0 5269.5306 10.590599
9500 16738.49 0 0 5269.5247 10.590554
9550 16738.484 0 0 5269.5226 10.590536
9600 16738.483 0 0 5269.5223 10.590534
9650 16738.464 0 0 5269.5165 10.590489
9700 16738.484 0 0 5269.5228 10.590537
9750 16738.507 0 0 5269.53 10.590595
9800 16738.482 0 0 5269.522 10.590532
9850 16738.478 0 0 5269.5207 10.590521
9900 16738.487 -0.00030979882 0 5269.5233 10.590538
9950 16738.476 -0.00095967357 0 5269.5193 10.590496
10000 16738.494 -0.00062714625 0 5269.5253 10.590548
Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms
Performance: 518773.777 tau/day, 60043.261 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 | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87
Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16
Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13
Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50
Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73
Other | | 0.006005 | | | 3.61
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 49 ave 49 max 49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

335
examples/rigid/log.20Apr18.rigid.nve.g++.4 Normal file
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@ -0,0 +1,335 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.69 571.70921 0 5265.8153 32.005816
100 16298.128 136.75661 0 5267.6488 16.449029
150 16682.532 17.504156 0 5269.4124 14.901186
200 16733.906 1.3755079 0 5269.4571 14.571305
250 16738.861 -0.15272039 0 5269.4886 14.498342
300 16738.608 -0.055216883 0 5269.5066 14.498
350 16738.5 -0.017457072 0 5269.5104 14.498392
400 16738.451 -0.0060161309 0 5269.5063 14.49851
450 16738.435 -0.001271965 0 5269.5059 14.498571
500 16738.443 -0.00081074175 0 5269.509 14.498598
550 16738.452 -0.00083208965 0 5269.5118 14.498618
600 16738.45 -0.00058358431 0 5269.5116 14.498617
650 16738.443 -0.00047228525 0 5269.5093 14.4986
700 16738.444 0 0 5269.5102 14.498612
750 16738.461 0 0 5269.5157 14.498654
800 16738.479 0 0 5269.521 14.498697
850 16738.473 0 0 5269.5192 14.498683
900 16738.449 0 0 5269.5116 14.498624
950 16738.438 -0.0035324203 0 5269.5046 14.498537
1000 16738.562 -0.051134242 0 5269.4963 14.498093
1050 16737.343 0.32970192 0 5269.4934 14.527634
1100 16737.878 0.16213235 0 5269.4941 14.533864
1150 16738.682 -0.089236256 0 5269.4959 14.511765
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
1250 16738.45 0 0 5269.5119 14.512611
1300 16738.475 0 0 5269.5199 14.512673
1350 16738.484 0 0 5269.5228 14.512696
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
1450 16738.45 -0.0010933363 0 5269.511 14.512595
1500 16738.445 -0.00057484239 0 5269.51 14.512591
1550 16738.451 0 0 5269.5123 14.512615
1600 16738.452 0 0 5269.5127 14.512618
1650 16738.443 0 0 5269.5099 14.512596
1700 16738.433 0 0 5269.5068 14.512572
1750 16738.438 0 0 5269.5084 14.512584
1800 16738.459 0 0 5269.5149 14.512635
1850 16738.473 0 0 5269.5193 14.51267
1900 16738.462 0 0 5269.5159 14.512644
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
2000 16738.463 -0.013425408 0 5269.5027 14.512382
2050 16738.535 -0.036964311 0 5269.5017 14.512152
2100 16738.621 -0.063490509 0 5269.5023 14.512108
2150 16738.594 -0.056143934 0 5269.5012 14.512117
2200 16738.536 -0.038486645 0 5269.5007 14.512277
2250 16738.496 -0.023712406 0 5269.503 14.51242
2300 16738.488 -0.013209094 0 5269.5109 14.51255
2350 16738.486 -0.0045244524 0 5269.519 14.512693
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
2550 16738.552 -0.04420046 0 5269.4998 14.512177
2600 16738.42 -0.004347531 0 5269.4982 14.512783
2650 16734.241 1.3131302 0 5269.5 14.577195
2700 16738.737 -0.10612056 0 5269.4961 14.503874
2750 16732.705 1.7939719 0 5269.4974 14.629294
2800 16738.558 -0.042867033 0 5269.5032 14.519893
2850 16738.499 -0.01271227 0 5269.5146 14.518524
2900 16738.486 -0.0032778045 0 5269.52 14.518712
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
3000 16738.647 -0.070862542 0 5269.5031 14.51803
3050 16678.313 18.829038 0 5269.409 15.533426
3100 16632.312 33.399217 0 5269.4975 14.588597
3150 16739.318 -0.31388148 0 5269.4715 13.520782
3200 16727.951 3.26736 0 5269.4741 12.288358
3250 16686.364 16.353793 0 5269.4682 14.152517
3300 16738.532 -0.031574462 0 5269.5064 13.310615
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
3450 16738.489 -0.021623738 0 5269.5026 13.308001
3500 16737.78 0.19719043 0 5269.4983 13.325999
3550 16658.578 25.116206 0 5269.4834 13.778249
3600 16738.51 -0.032864725 0 5269.4981 12.392389
3650 16738.899 -0.15952703 0 5269.4938 12.383503
3700 16738.879 -0.16025994 0 5269.487 12.382575
3750 16738.878 -0.16608251 0 5269.4806 12.382765
3800 16738.591 -0.078679341 0 5269.4776 12.383227
3850 16738.429 -0.024729409 0 5269.4807 12.382942
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
3950 16738.428 -0.002521266 0 5269.5027 12.383324
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
4050 16738.488 0 0 5269.5241 12.383531
4100 16738.468 0 0 5269.5178 12.383482
4150 16738.422 0 0 5269.5033 12.383369
4200 16738.387 0 0 5269.4921 12.383281
4250 16738.383 0 0 5269.4908 12.38327
4300 16738.4 0 0 5269.4964 12.383314
4350 16738.423 0 0 5269.5036 12.38337
4400 16738.441 0 0 5269.5092 12.383414
4450 16738.45 0 0 5269.5121 12.383437
4500 16738.45 0 0 5269.5122 12.383438
4550 16738.442 0 0 5269.5095 12.383417
4600 16738.425 0 0 5269.5042 12.383376
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
4700 16738.444 -0.024020551 0 5269.4862 12.382975
4750 16738.49 -0.048521424 0 5269.4761 12.385777
4800 16735.057 1.0347218 0 5269.4786 12.43543
4850 16735.441 0.92650925 0 5269.4913 12.418653
4900 16723.839 4.5908973 0 5269.5033 13.410103
4950 16738.531 -0.021537669 0 5269.5159 13.089982
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
5100 16738.404 0 0 5269.4976 13.090032
5150 16738.421 0 0 5269.5029 13.090073
5200 16738.44 0 0 5269.5087 13.090119
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
5300 16738.456 -0.0064376396 0 5269.5075 13.090026
5350 16738.479 -0.020383843 0 5269.5007 13.089898
5400 16735.845 0.79889489 0 5269.4909 13.136244
5450 16735.558 0.87619907 0 5269.4778 12.324482
5500 16711.494 8.4724273 0 5269.4984 12.656579
5550 16454.525 89.074821 0 5269.2031 16.996502
5600 16713.084 7.9801107 0 5269.5065 13.774972
5650 16738.676 -0.079987805 0 5269.5033 13.168292
5700 16446.281 91.866085 0 5269.399 23.764659
5750 16738.549 -0.039869082 0 5269.5034 13.378118
5800 16738.487 -0.014994465 0 5269.5086 13.378394
5850 16738.466 -0.0051267396 0 5269.512 13.378555
5900 16738.462 -0.004368998 0 5269.5113 13.378568
5950 16738.528 -0.032727397 0 5269.5039 13.378192
6000 16702.774 10.969422 0 5269.2502 13.788847
6050 16682.271 17.483223 0 5269.3092 13.353098
6100 16738.508 -0.028838294 0 5269.5016 12.521077
6150 16738.425 -0.0067595586 0 5269.4974 12.521216
6200 16738.401 -0.0011499906 0 5269.4955 12.521248
6250 16738.455 0 0 5269.5136 12.521404
6300 16738.523 0 0 5269.5352 12.521573
6350 16738.503 0 0 5269.5287 12.521525
6400 16738.427 0 0 5269.5047 12.521337
6450 16738.399 0 0 5269.496 12.521268
6500 16738.425 0 0 5269.5042 12.521331
6550 16738.441 0 0 5269.5093 12.521372
6600 16738.42 0 0 5269.5025 12.521319
6650 16738.398 0 0 5269.4957 12.521266
6700 16738.435 0 0 5269.5074 12.521355
6750 16738.505 0 0 5269.5293 12.521527
6800 16738.508 0 0 5269.5303 12.521536
6850 16738.446 0 0 5269.5108 12.521384
6900 16738.414 0 0 5269.5009 12.521306
6950 16738.432 0 0 5269.5063 12.521348
7000 16738.444 0 0 5269.5102 12.521379
7050 16738.421 0 0 5269.5029 12.521322
7100 16738.393 0 0 5269.4941 12.521253
7150 16738.419 0 0 5269.5022 12.521315
7200 16738.489 0 0 5269.5244 12.521489
7250 16738.505 0 0 5269.5293 12.521528
7300 16738.443 0 0 5269.5098 12.521377
7350 16738.404 0 0 5269.4976 12.521281
7400 16738.43 0 0 5269.5058 12.521344
7450 16738.461 0 0 5269.5156 12.521421
7500 16738.447 0 0 5269.5109 12.521385
7550 16738.407 0 0 5269.4986 12.521288
7600 16738.412 0 0 5269.5002 12.5213
7650 16738.478 0 0 5269.5208 12.521461
7700 16738.51 0 0 5269.5309 12.521541
7750 16738.454 0 0 5269.5135 12.521406
7800 16738.398 0 0 5269.4958 12.521267
7850 16738.407 -0.00021180715 0 5269.4982 12.521283
7900 16738.441 -0.0002167946 0 5269.509 12.521367
7950 16738.446 -0.0002384787 0 5269.5107 12.52138
8000 16738.423 0 0 5269.5035 12.521327
8050 16738.423 0 0 5269.5034 12.521325
8100 16738.478 -0.00069624484 0 5269.52 12.521448
8150 16738.523 -0.0040058183 0 5269.531 12.521494
8200 16738.486 -0.0092298512 0 5269.5142 12.521328
8250 16738.458 -0.023189661 0 5269.4914 12.521008
8300 16738.513 -0.045847765 0 5269.4861 12.520773
8350 16723.735 4.5720344 0 5269.4516 12.849543
8400 16738.466 -0.02019859 0 5269.497 12.835812
8450 16738.437 -0.012822198 0 5269.4952 12.829979
8500 16738.408 -0.0016833646 0 5269.4972 12.830104
8550 16738.464 -0.00097382606 0 5269.5155 12.830258
8600 16738.669 -0.050581176 0 5269.5304 12.829977
8650 15918.073 250.131 0 5261.3761 24.542327
8700 16738.446 0.00085039409 0 5269.5116 10.59114
8750 16738.472 -0.010146632 0 5269.5089 10.590059
8800 16738.468 0 0 5269.5176 10.590278
8850 16738.508 0 0 5269.5303 10.590378
8900 16738.509 0 0 5269.5306 10.590381
8950 16738.496 0 0 5269.5266 10.590349
9000 16738.477 0 0 5269.5204 10.590302
9050 16738.455 0 0 5269.5135 10.590247
9100 16738.477 0 0 5269.5205 10.590301
9150 16738.512 0 0 5269.5315 10.590388
9200 16738.502 0 0 5269.5285 10.590364
9250 16738.493 0 0 5269.5254 10.59034
9300 16738.482 0 0 5269.522 10.590314
9350 16738.46 0 0 5269.5151 10.59026
9400 16738.48 0 0 5269.5216 10.59031
9450 16738.509 0 0 5269.5306 10.590381
9500 16738.49 0 0 5269.5247 10.590335
9550 16738.484 0 0 5269.5226 10.590318
9600 16738.483 0 0 5269.5223 10.590316
9650 16738.464 0 0 5269.5165 10.590271
9700 16738.484 0 0 5269.5228 10.590319
9750 16738.507 0 0 5269.53 10.590376
9800 16738.482 0 0 5269.522 10.590314
9850 16738.478 0 0 5269.5207 10.590303
9900 16738.487 -0.00030979874 0 5269.5233 10.59032
9950 16738.476 -0.00095967134 0 5269.5192 10.590278
10000 16738.494 -0.00062714318 0 5269.5253 10.590329
Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms
Performance: 385008.767 tau/day, 44561.200 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78
Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58
Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15
Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04
Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94
Other | | 0.01013 | | | 4.51
Nlocal: 20.25 ave 34 max 9 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 38.5 ave 43 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0.75 ave 2 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 3
Ave neighs/atom = 0.037037
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

338
examples/rigid/log.20Apr18.rigid.poems.g++.1 Normal file
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.292 | 3.292 | 3.292 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699146
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538615
1350 20558.971 254.36482 0 3680.8601 -3.6773954
1400 21485.029 99.812918 0 3680.6511 -16.185473
1450 21771.107 52.159607 0 3680.6775 -2.4756675
1500 21520.948 93.503927 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.515995
1600 20778.805 216.92177 0 3680.0559 15.089187
1650 21477.638 100.21836 0 3679.8247 -1.1045739
1700 18501.339 596.47922 0 3680.0357 -15.679682
1750 18563.642 587.3479 0 3681.2882 33.532211
1800 19110.186 494.82336 0 3679.8543 18.024046
1850 21364.191 119.23543 0 3679.9339 2.5291075
1900 20146.627 322.14849 0 3679.9197 5.7313175
1950 20692.671 231.25345 0 3680.0319 4.297772
2000 20943.905 189.11218 0 3679.7629 -22.64509
2050 19668.055 401.83025 0 3679.8394 3.6251438
2100 20280.434 299.76289 0 3679.8353 7.4807805
2150 19181.835 483.52621 0 3680.4987 22.62081
2200 21300.18 130.7021 0 3680.7322 4.710193
2250 20486.914 266.64414 0 3681.1299 -8.6458025
2300 18653.082 572.25481 0 3681.1017 -5.2636982
2350 21513.563 95.608298 0 3681.2021 -9.3624751
2400 21466.205 103.57569 0 3681.2765 -29.559707
2450 20100.204 332.25468 0 3682.2886 35.739592
2500 20764.513 221.64794 0 3682.4001 -12.46688
2550 20436.771 276.13128 0 3682.2598 -22.419404
2600 21466.252 104.57185 0 3682.2806 -10.080362
2650 20817.269 212.81674 0 3682.3615 5.1374497
2700 18565.157 588.46125 0 3682.6541 22.283866
2750 20780.743 218.76366 0 3682.2208 -8.0046411
2800 21032.22 176.82368 0 3682.1936 -7.078895
2850 16817.729 879.49153 0 3682.4464 33.140849
2900 19309.511 463.89319 0 3682.145 7.9225025
2950 20544.978 257.86831 0 3682.0314 2.0523059
3000 20616.438 246.0975 0 3682.1706 -0.2824889
3050 18648.596 574.37266 0 3682.4721 -5.8677065
3100 19147.135 490.76826 0 3681.9574 -1.9922835
3150 18568.022 587.36965 0 3682.0399 14.694505
3200 19720.841 395.38315 0 3682.1899 5.9162402
3250 19008.557 514.50687 0 3682.5998 -3.4702895
3300 21708.937 64.231264 0 3682.3874 -5.4808611
3350 20548.477 257.62974 0 3682.3759 9.7818301
3400 20508.84 264.0153 0 3682.1553 -12.578182
3450 18736.579 559.11222 0 3681.8754 21.920437
3500 21444.82 107.82706 0 3681.9638 0.093050651
3550 20439.241 275.31015 0 3681.8503 -3.0785302
3600 21547.1 90.778361 0 3681.9617 -5.9189729
3650 15623.305 1079.996 0 3683.8802 36.064752
3700 19912.452 363.09483 0 3681.8368 5.4802367
3750 21289.7 133.2258 0 3681.5091 -10.884642
3800 20214.875 312.09245 0 3681.2382 8.6419893
3850 19853.031 372.13835 0 3680.9769 2.6229234
3900 17863.409 703.8716 0 3681.1064 -1.4250404
3950 19926.351 359.87227 0 3680.9307 -14.60997
4000 17595.665 747.85423 0 3680.4651 24.228859
4050 18408.194 611.80934 0 3679.8416 4.4236034
4100 17506.503 762.1286 0 3679.8792 5.0526379
4150 18479.134 600.76034 0 3680.6159 -6.6523095
4200 18475.322 601.95797 0 3681.1783 1.3292995
4250 18301.378 630.34119 0 3680.5709 2.5387332
4300 19384.541 449.98455 0 3680.7414 5.8750989
4350 18717.888 561.31715 0 3680.9651 3.7948584
4400 18893.773 532.20993 0 3681.172 10.963539
4450 20269.613 302.15984 0 3680.4286 -10.145642
4500 19151.762 489.32407 0 3681.2845 21.695364
4550 19914.708 361.54065 0 3680.6587 -4.2298372
4600 21153.44 154.99598 0 3680.5693 2.3172078
4650 21021.611 176.81454 0 3680.4164 1.9128023
4700 21707.966 62.767734 0 3680.762 -5.2080189
4750 16517.674 927.53839 0 3680.484 17.329608
4800 21654.604 71.574174 0 3680.6749 -6.0650166
4850 18135.978 657.28622 0 3679.9493 5.4803307
4900 20389.048 282.49215 0 3680.6668 -2.8570431
4950 17159.074 820.81472 0 3680.6604 31.273877
5000 20788.159 215.88415 0 3680.5773 4.6345196
5050 21366.767 119.68693 0 3680.8148 -9.9482889
5100 20668.21 236.17655 0 3680.8782 3.8118334
5150 20468.573 269.83696 0 3681.2657 -26.625943
5200 19493.142 432.49135 0 3681.3483 -7.6677112
5250 19626.594 410.09767 0 3681.1967 7.3622341
5300 20771.914 219.12484 0 3681.1105 -7.0871793
5350 21152.459 155.26401 0 3680.6738 5.9030557
5400 21376.189 117.91075 0 3680.6088 -1.2004513
5450 21455.06 105.15166 0 3680.995 -9.1675471
5500 21227.896 143.35739 0 3681.3401 -6.646305
5550 21149.831 156.61404 0 3681.5858 -12.953136
5600 21364.198 120.94695 0 3681.6466 1.0372254
5650 20219.777 311.34588 0 3681.3088 6.5026316
5700 21163.024 154.3001 0 3681.4708 -0.47587262
5750 19583.077 418.40745 0 3682.2535 24.609517
5800 18801.324 548.79742 0 3682.3515 -12.082631
5850 20875.4 203.07604 0 3682.3093 -8.1191161
5900 20737.053 226.2734 0 3682.4489 -7.6845943
5950 21260.028 139.21888 0 3682.5568 -2.2977046
6000 19823.84 378.71803 0 3682.6914 -1.1163373
6050 20487.214 268.03474 0 3682.5704 4.313979
6100 17853.211 707.10918 0 3682.6443 16.762322
6150 21322.705 129.06 0 3682.8441 2.7500936
6200 21609.008 81.580972 0 3683.0823 0.37062555
6250 20364.115 289.30707 0 3683.3262 13.176034
6300 20201.9 316.16558 0 3683.149 -1.6318339
6350 21151.879 157.75018 0 3683.0634 -23.337621
6400 21453.129 107.45563 0 3682.9772 -0.60776225
6450 21105.382 165.1926 0 3682.7562 4.244932
6500 20746.748 224.6945 0 3682.4859 0.2929158
6550 20913.725 197.29847 0 3682.9194 -15.792862
6600 17956.374 690.52623 0 3683.2552 15.445255
6650 20270.609 303.60078 0 3682.0357 -0.26503277
6700 21442.931 109.08904 0 3682.9109 -2.8409166
6750 20907.994 198.30695 0 3682.9726 0.91664072
6800 20431.208 277.98326 0 3683.1845 -1.8537161
6850 20312.052 297.88656 0 3683.2285 3.1028547
6900 19458.401 439.97157 0 3683.0385 -4.1856293
6950 20507.759 264.99217 0 3682.952 -1.4597973
7000 20782.356 219.47456 0 3683.2006 -7.1967021
7050 20560.324 256.07109 0 3682.7917 -10.720013
7100 21652.145 74.086415 0 3682.7772 -0.61455054
7150 20134.823 326.40272 0 3682.2065 11.689827
7200 20778.071 219.16459 0 3682.1765 -1.796567
7250 20153.065 323.13721 0 3681.9814 -0.1215538
7300 19524.938 427.99711 0 3682.1534 -3.1139903
7350 20554.595 256.63855 0 3682.4044 10.023083
7400 18778.53 552.29852 0 3682.0534 -1.7145222
7450 18972.509 520.15393 0 3682.2388 1.4489874
7500 17680.668 736.20139 0 3682.9794 15.096954
7550 19070.785 504.65403 0 3683.1182 2.2707533
7600 20805.541 214.54957 0 3682.1398 -3.4306308
7650 18473.262 604.25322 0 3683.1301 2.2083367
7700 19294.016 466.99211 0 3682.6615 2.2666382
7750 20995.664 183.47108 0 3682.7484 -13.935938
7800 21042.433 175.06619 0 3682.1384 0.49855811
7850 19343.054 459.21955 0 3683.0618 7.9049312
7900 18382.898 619.01969 0 3682.8361 1.7996366
7950 16092.435 1000.6563 0 3682.7287 29.993154
8000 17551.635 757.47719 0 3682.7498 8.1753011
8050 20309.875 298.25877 0 3683.2379 -1.9545317
8100 21746.174 59.002125 0 3683.3645 -2.6980678
8150 21478.427 103.44202 0 3683.1799 -10.930392
8200 20986.729 185.46995 0 3683.2581 -14.298403
8250 20744.064 225.47546 0 3682.8194 -6.4982356
8300 19887.982 368.35069 0 3683.0143 1.5899179
8350 21871.414 37.899202 0 3683.1348 -2.0554107
8400 20002.858 348.98887 0 3682.7985 8.2963084
8450 21553.861 90.985193 0 3683.2953 2.8575186
8500 21605.143 82.347635 0 3683.2048 -4.711565
8550 20151.76 324.4703 0 3683.097 -8.5109459
8600 20564.158 255.77814 0 3683.1378 -1.3815408
8650 19316.602 463.61706 0 3683.0507 -2.6895635
8700 18157.859 656.69518 0 3683.0051 19.428927
8750 18752.43 557.67555 0 3683.0805 1.9765973
8800 20903.812 199.07408 0 3683.0428 1.9011523
8850 20132.963 327.56826 0 3683.0621 3.0389961
8900 21667.171 71.80023 0 3682.9954 -2.0042246
8950 20346.973 292.00907 0 3683.1712 7.5582361
9000 17889.448 695.59406 0 3677.1688 7.5315391
9050 19446.144 441.90609 0 3682.9302 5.9819228
9100 20384.34 285.05862 0 3682.4486 9.8610378
9150 20023.515 344.98587 0 3682.2384 -0.40175043
9200 17786.795 718.76166 0 3683.2275 10.984317
9250 20843.023 208.42263 0 3682.2597 -7.4709344
9300 21670.622 70.503925 0 3682.2742 -6.2303366
9350 20642.313 241.21277 0 3681.5983 4.7423898
9400 19228.566 476.44753 0 3681.2085 10.836639
9450 21215.705 146.40003 0 3682.3509 -9.091421
9500 21543.685 91.725901 0 3682.3401 -1.0608492
9550 20143.22 324.98532 0 3682.1887 -5.995164
9600 21234.294 142.96512 0 3682.0142 0.004838125
9650 21025.207 177.8801 0 3682.0813 -5.4857701
9700 20638.235 242.46577 0 3682.1716 -1.6014085
9750 18374.191 620.54322 0 3682.9084 13.864712
9800 19730.262 393.89083 0 3682.2679 5.7601754
9850 21547.855 91.283379 0 3682.5926 2.1989329
9900 20959.935 189.28821 0 3682.6108 2.1174676
9950 21191.026 150.79441 0 3682.6321 8.3829825
10000 20776.574 220.03769 0 3682.8 -1.8404787
Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms
Performance: 28004.636 tau/day, 3241.277 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62
Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55
Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33
Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10
Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05
Other | | 0.01105 | | | 0.36
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 82 ave 82 max 82 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 887 ave 887 max 887 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 887
Ave neighs/atom = 10.9506
Neighbor list builds = 992
Dangerous builds = 939
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.263 | 3.357 | 3.638 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699147
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538614
1350 20558.971 254.36483 0 3680.8601 -3.6773951
1400 21485.029 99.812917 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503926 0 3680.3286 2.1023576
1550 21351.418 121.68137 0 3680.2511 5.5159947
1600 20778.805 216.92177 0 3680.0559 15.089188
1650 21477.638 100.21836 0 3679.8247 -1.1045741
1700 18501.339 596.4792 0 3680.0357 -15.679682
1750 18563.642 587.34785 0 3681.2882 33.53221
1800 19110.185 494.82342 0 3679.8543 18.024046
1850 21364.191 119.23548 0 3679.9339 2.5291079
1900 20146.626 322.14873 0 3679.9197 5.7313282
1950 20692.672 231.2533 0 3680.0319 4.2977759
2000 20943.904 189.11231 0 3679.7629 -22.645089
2050 19668.052 401.83077 0 3679.8394 3.6251598
2100 20280.434 299.76292 0 3679.8353 7.4807838
2150 19181.841 483.52513 0 3680.4987 22.620829
2200 21300.185 130.70136 0 3680.7321 4.7101928
2250 20486.897 266.64698 0 3681.1299 -8.6459184
2300 18653.018 572.26538 0 3681.1017 -5.2635489
2350 21513.576 95.606125 0 3681.202 -9.3627078
2400 21466.185 103.579 0 3681.2764 -29.55912
2450 20100.274 332.24291 0 3682.2886 35.736349
2500 20764.562 221.63964 0 3682.4 -12.465656
2550 20437.187 276.06174 0 3682.2596 -22.421308
2600 21466.269 104.56898 0 3682.2805 -10.080867
2650 20819.865 212.38395 0 3682.3615 5.1305357
2700 18565.57 588.39438 0 3682.656 22.28768
2750 20789.153 217.36229 0 3682.2211 -8.051962
2800 21045.639 174.58656 0 3682.193 -7.0803377
2850 16845.227 874.90505 0 3682.4429 32.992098
2900 19319.232 462.27119 0 3682.1432 7.9276373
2950 20558.495 255.61185 0 3682.0277 1.9151653
3000 20615.868 246.18886 0 3682.1668 -0.016805532
3050 18695.136 566.5914 0 3682.4474 -7.3528355
3100 19381.554 451.57712 0 3681.8361 -2.0887636
3150 19080.633 502.00742 0 3682.1129 5.2518182
3200 20969.083 187.13559 0 3681.9828 12.156446
3250 20474.81 269.6876 0 3682.156 1.4067779
3300 18836.313 542.79266 0 3682.1781 -9.1497216
3350 21397.694 116.27473 0 3682.557 -6.4412585
3400 20886.812 201.52507 0 3682.6604 6.3038335
3450 21604.639 81.93055 0 3682.7038 2.3769444
3500 20847.621 207.85705 0 3682.4605 -2.758021
3550 20627.979 244.69999 0 3682.6964 -0.33497747
3600 19265.519 471.27582 0 3682.1956 2.3506222
3650 20351.848 290.65727 0 3682.6319 3.5445062
3700 18507.473 597.72931 0 3682.3082 -21.283074
3750 20344.017 291.60622 0 3682.2757 6.5366987
3800 20672.372 237.18966 0 3682.585 6.7310703
3850 21366.943 122.07461 0 3683.2318 -3.5870721
3900 20890.294 201.69901 0 3683.4147 -9.5644117
3950 20684.181 235.91733 0 3683.2809 -4.8913079
4000 21499.086 100.67563 0 3683.8566 1.1969651
4050 18549.152 590.04529 0 3681.5707 -9.1914883
4100 18436.457 604.2601 0 3677.003 3.6486137
4150 19332.655 462.03124 0 3684.1404 -11.280758
4200 21199.837 150.66602 0 3683.9722 0.14505208
4250 19088.228 501.77395 0 3683.1453 1.6869973
4300 16617.942 913.86736 0 3683.5244 9.1792322
4350 19765.761 388.52744 0 3682.821 -4.1982973
4400 20181.964 320.06096 0 3683.7216 5.3685715
4450 20132.04 328.29106 0 3683.631 6.3340995
4500 21026.359 179.13858 0 3683.5317 -15.365253
4550 19273.765 471.36221 0 3683.6564 -0.71397595
4600 20064.71 339.29348 0 3683.4117 -4.8121056
4650 19821.01 380.27685 0 3683.7784 11.857115
4700 18724.367 563.42963 0 3684.1575 13.250333
4750 20467.467 273.2046 0 3684.449 -1.8076823
4800 19630.315 412.48507 0 3684.2042 -9.0412254
4850 19483.424 437.0206 0 3684.258 11.22465
4900 18504.179 600.28485 0 3684.3146 -5.2345686
4950 21436.13 111.62139 0 3684.3098 -5.8197915
5000 18022.817 680.57727 0 3684.38 19.238942
5050 20750.212 226.15635 0 3684.525 -0.73974419
5100 20569.533 255.21358 0 3683.4691 -18.332775
5150 21447.046 109.3048 0 3683.8124 -2.5745966
5200 18985.753 519.77191 0 3684.0641 9.7821968
5250 21334.568 128.16597 0 3683.9273 -0.61310451
5300 18836.476 544.54018 0 3683.9528 -17.979429
5350 18574.391 587.20088 0 3682.9327 40.990206
5400 21003.047 183.40176 0 3683.9096 6.1115776
5450 20693.875 234.62783 0 3683.607 5.4472209
5500 17673.479 738.99306 0 3684.5729 -28.621738
5550 19265.837 472.34663 0 3683.3195 -6.609151
5600 20800.947 217.12409 0 3683.9486 2.6477049
5650 21746.371 59.453265 0 3683.8485 1.5272163
5700 20448.97 275.57425 0 3683.736 -7.9864104
5750 19776.152 387.64417 0 3683.6695 -16.604848
5800 15779.293 1055.4995 0 3685.3817 20.365883
5850 21008.009 182.52093 0 3683.8557 -6.6727217
5900 21566.123 89.588216 0 3683.9421 -7.8944316
5950 21591.695 85.284975 0 3683.9009 -2.4895203
6000 17737.17 726.79112 0 3682.9861 1.5643841
6050 16648.524 907.73295 0 3682.487 3.0853478
6100 19917.439 363.6324 0 3683.2056 4.358303
6150 21767.004 56.152017 0 3683.986 -8.8722559
6200 17654.098 742.15421 0 3684.5039 9.7673482
6250 20125.754 329.65218 0 3683.9445 5.5050658
6300 20160.047 323.44453 0 3683.4524 4.852504
6350 20509.459 264.29515 0 3682.5383 2.5335834
6400 17199.686 817.09171 0 3683.7061 8.3428304
6450 18748.366 558.82243 0 3683.5501 0.23782614
6500 19133.519 494.28383 0 3683.2037 8.1586096
6550 20311.228 297.30741 0 3682.5122 -1.7015056
6600 18879.49 536.62652 0 3683.2082 5.0874769
6650 18189.35 651.42447 0 3682.9828 -15.223564
6700 19925.861 361.90598 0 3682.8828 0.26811015
6750 19420.312 445.30915 0 3682.0278 5.5725626
6800 19925.024 361.87412 0 3682.7114 -3.9763013
6850 16196.938 985.7242 0 3685.2138 2.8265047
6900 19779.752 386.51634 0 3683.1416 16.798629
6950 21043.144 176.83133 0 3684.0221 -4.193188
7000 18555.362 589.47043 0 3682.0307 14.516315
7050 21225.883 147.54974 0 3685.1969 -13.466586
7100 21234.667 145.92615 0 3685.0373 -5.1951121
7150 21483.472 104.62556 0 3685.2042 -5.6904048
7200 21014.278 182.97687 0 3685.3566 1.044649
7250 18588.789 587.96259 0 3686.094 22.707132
7300 20202.932 318.14401 0 3685.2994 -10.795766
7350 18304.22 634.7344 0 3685.4377 -1.6801482
7400 20967.579 190.67822 0 3685.2747 -0.94800692
7450 20991.588 186.07163 0 3684.6696 -1.411476
7500 19056.583 507.18197 0 3683.2791 3.2026014
7550 18542.455 594.92944 0 3685.3386 -27.908724
7600 19895.73 367.08589 0 3683.0409 4.1334366
7650 20384.942 285.88041 0 3683.3707 -7.515362
7700 20683.189 235.46294 0 3682.6611 10.876437
7750 20729.325 228.204 0 3683.0915 3.8844308
7800 21667.475 71.752748 0 3682.9985 -15.457992
7850 19043.652 508.96807 0 3682.9101 -5.8335792
7900 21079.827 169.61123 0 3682.9158 -1.3216223
7950 20713.266 230.43917 0 3682.6502 -0.20026535
8000 20606.41 248.06357 0 3682.4652 4.2844844
8050 20284.503 302.0469 0 3682.7973 6.3402329
8100 21859.537 39.514865 0 3682.7711 -13.302141
8150 18495.181 600.26329 0 3682.7934 9.9318242
8200 21458.549 105.63828 0 3682.0631 -7.7419285
8250 18704.511 564.30958 0 3681.728 14.680489
8300 20689.366 233.57049 0 3681.7982 2.3067527
8350 20692.974 232.67005 0 3681.499 4.2743386
8400 20240.086 307.5395 0 3680.8872 1.9694217
8450 19075.969 501.34689 0 3680.6751 11.056078
8500 21456.727 103.36067 0 3679.4818 -3.4512371
8550 20393.16 279.84781 0 3678.7078 6.3282998
8600 20898.88 195.43751 0 3678.5842 -14.393947
8650 20297.482 295.3169 0 3678.2306 -0.96829147
8700 21079.56 164.72934 0 3677.9893 -8.339122
8750 21142.519 154.18527 0 3677.9384 -4.6169442
8800 20143.871 320.23161 0 3677.5435 6.5710426
8850 21030.065 172.88831 0 3677.8992 1.3973883
8900 19814.648 375.22097 0 3677.6624 2.6996208
8950 17392.382 778.87517 0 3677.6055 11.963975
9000 19209.163 476.44659 0 3677.9738 8.7050034
9050 20143.824 320.17051 0 3677.4745 -5.8044332
9100 21400.78 110.99404 0 3677.7908 -3.0027429
9150 21834.471 38.970732 0 3678.0493 -2.5838117
9200 21344.715 120.55831 0 3678.0108 4.8187829
9250 20998.277 178.31959 0 3678.0324 -1.2009012
9300 21141.788 154.4658 0 3678.0971 -21.693564
9350 21439.398 105.00432 0 3678.2374 -16.113694
9400 21296.282 128.83877 0 3678.2191 -2.9990284
9450 19050.623 503.10319 0 3678.207 15.622525
9500 20845.847 203.77117 0 3678.079 -1.7504827
9550 18808.956 543.38757 0 3678.2135 -2.6611868
9600 20612.559 242.57373 0 3678.0002 -0.1650541
9650 20522.637 257.28926 0 3677.7288 6.8876074
9700 20970.074 182.75754 0 3677.7699 -4.5350279
9750 18297.505 625.06808 0 3674.6522 32.429153
9800 21042.472 170.78969 0 3677.8684 5.4901963
9850 20444.092 270.84839 0 3678.197 6.9444494
9900 21597.787 78.901871 0 3678.533 2.3445932
9950 18376.854 616.35469 0 3679.1636 -8.55063
10000 21490.054 97.234379 0 3678.9101 -0.36115606
Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms
Performance: 25554.943 tau/day, 2957.748 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 | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29
Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86
Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44
Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21
Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24
Other | | 0.03255 | | | 0.96
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 45.5 ave 82 max 12 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 218.75 ave 875 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 875
Ave neighs/atom = 10.8025
Neighbor list builds = 993
Dangerous builds = 945
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:363)
WARNING: More than one fix poems (../fix_poems.cpp:363)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.854 | 3.854 | 3.854 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.92346
1500 19223.688 204.15177 0 3764.0939 -1.6134528
1550 18147.996 404.12677 0 3764.8668 8.4194783
1600 18615.043 317.42469 0 3764.6548 -2.3288917
1650 20120.654 38.887903 0 3764.935 -8.7620301
1700 19450.907 162.98262 0 3765.0025 2.3254748
1750 19374.631 177.37975 0 3765.2744 8.9328771
1800 19424.404 167.93963 0 3765.0514 0.081227378
1850 17936.203 442.85082 0 3764.3699 6.6011902
1900 19982.595 64.406292 0 3764.8868 -2.95296
1950 16215.781 761.92636 0 3764.8487 13.995056
2000 18584.444 322.1163 0 3763.6801 7.1653369
2050 20107.965 41.025841 0 3764.723 -0.31088772
2100 20002.324 60.594786 0 3764.7288 -6.7919989
2150 16949.875 626.57523 0 3765.4409 3.50855
2200 20010.954 58.808121 0 3764.5403 -10.862112
2250 18982.734 247.00818 0 3762.3293 -0.53817452
2300 18401.254 354.88774 0 3762.5274 1.0921595
2350 19390.545 172.93755 0 3763.7793 -3.3523777
2400 16080.137 786.51156 0 3764.3147 -16.202632
2450 18870.17 268.79443 0 3763.2704 11.201845
2500 19688.736 117.49945 0 3763.5616 4.3786781
2550 18869.811 268.97474 0 3763.3842 -5.6659314
2600 17021.088 611.38597 0 3763.4393 6.3051835
2650 18743.998 292.7827 0 3763.8934 2.4233167
2700 19745.629 106.63088 0 3763.2289 -0.34816161
2750 19527.584 147.21131 0 3763.4306 -1.6219417
2800 18195.354 392.99533 0 3762.5053 24.376674
2850 18550.094 327.77867 0 3762.9812 4.2654596
2900 20174.105 27.269108 0 3763.2144 1.7109311
2950 17744.679 476.70478 0 3762.7564 0.46336417
3000 19161.715 214.56545 0 3763.0311 2.3774967
3050 18357.87 363.54089 0 3763.1465 7.5885138
3100 18851.02 272.19735 0 3763.1269 8.0560784
3150 19586.208 136.32381 0 3763.3995 -10.118566
3200 19300.444 189.2076 0 3763.3639 -12.590066
3250 18680.955 303.88073 0 3763.3168 -1.0138975
3300 18444.612 347.49752 0 3763.1664 8.9271155
3350 19006.554 243.54359 0 3763.2757 4.7398999
3400 17842.797 459.11352 0 3763.3351 28.63048
3450 19801.317 96.103613 0 3763.0141 4.0933253
3500 18599.338 318.61343 0 3762.9353 6.3657111
3550 19737.266 107.84071 0 3762.89 1.3861757
3600 19002.648 244.0525 0 3763.0613 8.7615304
3650 19154.418 215.94396 0 3763.0584 -2.6243193
3700 19036.117 237.84014 0 3763.047 -5.6841944
3750 20045.863 50.759281 0 3762.9562 -2.1930939
3800 19331.877 182.69303 0 3762.6703 0.57474959
3850 18193.947 393.70074 0 3762.9502 -4.1144639
3900 19675.638 119.2295 0 3762.8663 0.46172332
3950 19506.743 150.36614 0 3762.7259 5.8020668
4000 17985.008 431.80897 0 3762.366 10.755615
4050 19947.208 68.962683 0 3762.8902 -2.0041629
4100 19936.06 70.997196 0 3762.8602 -6.6295574
4150 19011.006 242.10402 0 3762.6608 -12.682711
4200 18108.183 409.44214 0 3762.8094 -0.42654932
4250 18734.162 293.70086 0 3762.9901 8.8549986
4300 16619.218 686.30953 0 3763.9426 43.405681
4350 18818.184 277.95188 0 3762.8007 20.953883
4400 18649.616 307.93211 0 3761.5647 -3.6011031
4450 18626.995 313.23564 0 3762.6792 -2.5430627
4500 18133.284 405.27778 0 3763.2934 3.057056
4550 19985.929 61.792735 0 3762.8908 1.9540846
4600 18664.305 306.02805 0 3762.3809 1.2395242
4650 19822.408 92.030223 0 3762.8466 -1.0496216
4700 19218.014 203.93895 0 3762.8305 0.74203538
4750 19425.781 165.36374 0 3762.7306 4.0113982
4800 18604.891 317.55244 0 3762.9026 16.671366
4850 19648.156 124.29963 0 3762.8471 4.1073
4900 18928.508 257.76023 0 3763.0394 -4.3547566
4950 19795.841 97.135231 0 3763.0317 -10.401888
5000 20150.671 31.452661 0 3763.0584 -3.352706
5050 18694.789 300.8954 0 3762.8933 11.690808
5100 16936.745 627.00902 0 3763.4434 -0.56880353
5150 18446.99 346.49004 0 3762.5992 8.409244
5200 18532.691 330.61677 0 3762.5966 10.358529
5250 18342.743 366.3264 0 3763.1306 -9.5622676
5300 20038.203 52.234825 0 3763.0131 -3.6974868
5350 19337.092 182.06755 0 3763.0106 -0.045248915
5400 19561.005 140.5518 0 3762.9602 1.3850963
5450 19415.557 167.29181 0 3762.7654 2.6966013
5500 18646.823 309.81657 0 3762.9319 7.4858844
5550 19165.312 214.07271 0 3763.2046 1.4335924
5600 18879.507 266.90953 0 3763.1146 7.8746695
5650 19824.482 91.786842 0 3762.9872 -2.4395467
5700 19699.85 114.8239 0 3762.9442 4.2779932
5750 19535.697 145.24886 0 3762.9706 5.9452722
5800 18275.446 378.66191 0 3763.0038 11.965062
5850 19931.992 71.873259 0 3762.9828 -2.3097575
5900 18528.705 331.64793 0 3762.8897 -18.312104
5950 16535.446 701.02536 0 3763.1451 -14.797902
6000 18678.807 303.76763 0 3762.806 -3.2732626
6050 16661.525 677.73561 0 3763.2031 17.862761
6100 18100.317 410.39139 0 3762.3019 -4.9765779
6150 16487.861 707.08907 0 3760.3967 32.53899
6200 16823.279 647.56578 0 3762.9878 -9.8237219
6250 18418.096 351.89624 0 3762.6548 -2.0149855
6300 18822.067 277.01314 0 3762.5811 5.3782716
6350 19300.198 188.57243 0 3762.6832 -1.9316023
6400 18425.789 350.70367 0 3762.8868 2.6884393
6450 18708.506 297.50643 0 3762.0447 -13.808707
6500 19528.099 146.10805 0 3762.4226 -1.5991505
6550 19701.841 114.01327 0 3762.5023 4.4322487
6600 18892.934 262.83827 0 3761.5297 10.689265
6650 19041.669 235.52692 0 3761.7619 -1.1425512
6700 19352.162 178.40501 0 3762.1388 -0.55130997
6750 16177.653 765.61942 0 3761.481 4.6526477
6800 19007.323 242.63753 0 3762.5122 3.6202242
6850 14255.206 1125.4974 0 3765.3503 -31.10433
6900 18481.408 340.4703 0 3762.9532 0.53246054
6950 19227.569 202.33363 0 3762.9946 -0.94126626
7000 18771.85 286.70279 0 3762.9714 3.151759
7050 18689.51 301.95602 0 3762.9765 8.0511724
7100 18599.258 318.83229 0 3763.1394 -0.86222116
7150 17739.189 478.35458 0 3763.3896 11.976827
7200 19492.829 153.62536 0 3763.4084 -8.6815909
7250 18797.718 282.17319 0 3763.232 -19.897633
7300 18353.871 364.09362 0 3762.9585 5.4538454
7350 19040.053 237.34144 0 3763.2772 6.5600248
7400 19452.586 160.98629 0 3763.317 -9.0542585
7450 19033.845 238.45033 0 3763.2365 3.2654681
7500 18137.358 404.80969 0 3763.5796 -7.2639486
7550 16863.391 642.47654 0 3765.3267 31.248679
7600 16374.538 731.74039 0 3764.0622 29.566291
7650 19837.917 89.823014 0 3763.5114 -2.6605403
7700 15593.154 876.08807 0 3763.7093 -9.7668717
7750 16609.929 687.32679 0 3763.2396 1.0775966
7800 17513.384 519.87756 0 3763.0968 3.4979836
7850 20022.015 56.036771 0 3763.8173 -4.316185
7900 17681.324 489.71547 0 3764.0347 5.1978443
7950 18320.382 371.17872 0 3763.8421 6.1860655
8000 20014.059 57.688322 0 3763.9956 -9.0623854
8050 16203.013 762.61545 0 3763.1735 31.662714
8100 18749.745 291.57889 0 3763.7538 -14.015057
8150 19411.326 169.05845 0 3763.7485 -4.3392799
8200 17994.991 431.56932 0 3763.9751 6.8158642
8250 19325.923 185.1137 0 3763.9883 9.4923883
8300 17354.302 550.33316 0 3764.0927 6.1636399
8350 19900.895 78.431831 0 3763.7828 -4.5224196
8400 17775.757 471.62915 0 3763.4361 12.949899
8450 19909.324 76.935162 0 3763.8471 -2.950115
8500 18601.933 318.79405 0 3763.5965 6.0173542
8550 18685.758 303.59497 0 3763.9205 2.7277487
8600 19297.521 190.12606 0 3763.741 4.8998933
8650 17396.37 542.14326 0 3763.6932 39.937715
8700 17134.714 590.99465 0 3764.0898 10.37328
8750 14348.104 1106.7544 0 3763.8106 -3.8604659
8800 19830.924 90.929138 0 3763.3225 0.26603444
8850 18551.537 326.53747 0 3762.0072 -1.5369982
8900 20040.322 52.066026 0 3763.2367 -12.667979
8950 19314.585 186.54793 0 3763.3228 -0.64755555
9000 19117.66 222.84553 0 3763.153 5.2990011
9050 19072.016 231.26038 0 3763.1152 -1.6513695
9100 19284.933 191.73976 0 3763.0237 -3.932358
9150 17356.576 548.61808 0 3762.7988 1.3659056
9200 18939.549 255.43703 0 3762.761 3.3037106
9250 19621.961 129.5012 0 3763.1976 1.667
9300 16898.033 633.79921 0 3763.0647 7.5941845
9350 19662.75 122.10836 0 3763.3584 -3.3144828
9400 16118.338 778.70243 0 3763.5799 9.8684537
9450 17362.374 548.18847 0 3763.443 6.8117548
9500 17873.057 453.37389 0 3763.1993 9.5651746
9550 19282.305 192.593 0 3763.3901 -4.987757
9600 18236.48 386.36263 0 3763.4886 8.8658343
9650 17695.571 486.6517 0 3763.6093 12.471421
9700 19044.003 237.04652 0 3763.7138 0.84430497
9750 17937.299 442.4372 0 3764.1592 3.981475
9800 18179.761 396.86987 0 3763.4923 -11.397273
9850 19157.292 215.8937 0 3763.5404 -7.7648682
9900 19719.066 111.98124 0 3763.6602 5.5378968
9950 18103.235 410.65473 0 3763.1056 28.201374
10000 18479.903 341.32548 0 3763.5297 -5.0581298
Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms
Performance: 27486.104 tau/day, 3181.262 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88
Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46
Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39
Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10
Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80
Other | | 0.01151 | | | 0.37
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 67 ave 67 max 67 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 599 ave 599 max 599 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 599
Ave neighs/atom = 7.39506
Neighbor list builds = 993
Dangerous builds = 945
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

342
examples/rigid/log.20Apr18.rigid.poems2.g++.4 Normal file
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:363)
WARNING: More than one fix poems (../fix_poems.cpp:363)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
Neighbor list info ...
update every 1 steps, delay 10 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 = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 3.825 | 3.919 | 4.201 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15172 0 3764.0939 -1.6134536
1550 18147.996 404.12676 0 3764.8668 8.4194774
1600 18615.043 317.42466 0 3764.6548 -2.3288957
1650 20120.654 38.887927 0 3764.935 -8.7620244
1700 19450.906 162.98284 0 3765.0025 2.3254707
1750 19374.632 177.37954 0 3765.2744 8.9328778
1800 19424.403 167.93971 0 3765.0514 0.081234023
1850 17936.311 442.83087 0 3764.3699 6.600894
1900 19982.596 64.40607 0 3764.8868 -2.9530102
1950 16215.95 761.89459 0 3764.8482 13.994238
2000 18584.39 322.12621 0 3763.68 7.1654863
2050 20107.966 41.025634 0 3764.723 -0.31093298
2100 20002.346 60.590652 0 3764.7288 -6.7919499
2150 16949.612 626.62391 0 3765.441 3.5094585
2200 20010.952 58.808492 0 3764.5403 -10.862255
2250 18982.727 247.00941 0 3762.3292 -0.53796622
2300 18401.351 354.86992 0 3762.5275 1.0919209
2350 19390.5 172.94589 0 3763.7793 -3.3526281
2400 16081.648 786.23133 0 3764.3143 -16.197875
2450 18870.722 268.69249 0 3763.2707 11.192419
2500 19687.71 117.6898 0 3763.562 4.387789
2550 18872.129 268.54506 0 3763.3838 -5.6577428
2600 17017.179 612.11028 0 3763.4397 6.3187623
2650 18766.343 288.63699 0 3763.8856 2.3968008
2700 19737.998 108.02069 0 3763.2054 -0.30752024
2750 19508.797 150.69812 0 3763.4384 -1.6171126
2800 18394.822 355.73011 0 3762.1787 21.193311
2850 18561.108 325.76417 0 3763.0065 3.9331499
2900 20124.042 36.554163 0 3763.2286 0.54133121
2950 15727.607 849.90471 0 3762.4245 13.885323
3000 17991.206 431.32693 0 3763.0317 9.9953567
3050 18834.86 275.34241 0 3763.2795 9.1519305
3100 18986.272 247.38123 0 3763.3575 -1.8754521
3150 19979.145 63.575968 0 3763.4177 -11.800026
3200 19953.846 68.376593 0 3763.5332 -6.7719573
3250 15646.02 867.19502 0 3764.6062 16.433911
3300 16946.252 625.14854 0 3763.3433 4.3975456
3350 19006.567 243.97026 0 3763.7048 5.3392405
3400 18082.133 414.87059 0 3763.4138 15.143954
3450 18273.719 379.36162 0 3763.3836 5.4465204
3500 19783.17 100.06678 0 3763.6167 1.9588505
3550 19794.99 97.904519 0 3763.6435 -3.0349395
3600 18357.708 363.98291 0 3763.5585 -2.1229788
3650 19647.179 125.48949 0 3763.8559 1.2967845
3700 18806.632 281.78709 0 3764.4967 5.125718
3750 18982.747 248.97053 0 3764.294 -0.72036085
3800 19597.926 135.04805 0 3764.2935 -3.2129291
3850 18914.042 261.7133 0 3764.3136 -12.163282
3900 18646.326 311.16482 0 3764.1881 5.1808943
3950 18589.554 321.36256 0 3763.8726 4.9554103
4000 17877.615 453.02456 0 3763.694 9.8457113
4050 19440.059 164.15739 0 3764.1684 -5.4054486
4100 18505.545 337.36023 0 3764.313 4.8468985
4150 19220.307 204.85944 0 3764.1755 -6.5040818
4200 19058.915 234.79578 0 3764.2245 3.1852011
4250 19867.025 85.136186 0 3764.2149 5.6156236
4300 16989.857 616.86564 0 3763.1355 -3.4041875
4350 19782.09 100.85847 0 3764.2085 3.2531098
4400 19879.56 82.559198 0 3763.9593 1.6340828
4450 19409.95 169.46676 0 3763.9019 -1.824265
4500 19742.977 107.72786 0 3763.8347 -0.72711698
4550 17166.529 585.04113 0 3764.028 -0.38806102
4600 19604.596 133.61426 0 3764.0949 -5.2712214
4650 18865.608 270.23956 0 3763.8707 1.5751363
4700 20190.139 25.270932 0 3764.1855 -10.159924
4750 20043.487 52.56327 0 3764.3201 -4.713579
4800 19361.931 178.70311 0 3764.246 4.2460799
4850 19460.365 160.29083 0 3764.0621 3.5079181
4900 18252.89 384.16194 0 3764.3268 4.1870604
4950 19516.947 150.07365 0 3764.3231 4.0238527
5000 19041.145 238.27335 0 3764.4113 8.2280019
5050 19519.408 149.66793 0 3764.3731 -0.088904966
5100 18087.848 415.34004 0 3764.9416 8.9482852
5150 19392.463 173.43121 0 3764.628 -6.6722716
5200 19683.968 119.46663 0 3764.6458 -2.0330852
5250 19675.404 121.09497 0 3764.6884 3.0627309
5300 18627.53 314.96107 0 3764.5038 5.2692141
5350 20022.616 56.725346 0 3764.6172 -7.7034469
5400 19353.4 180.6482 0 3764.6112 -2.3897589
5450 16966.649 622.29693 0 3764.2689 6.3601638
5500 17584.292 508.42495 0 3764.7753 5.949219
5550 19169.69 214.76864 0 3764.7113 3.3778997
5600 19491.814 155.19149 0 3764.7866 -0.20031164
5650 19079.585 231.70394 0 3764.9605 7.3017226
5700 19686.564 119.34 0 3765 0.98980357
5750 19639.909 127.89886 0 3764.919 2.3982612
5800 19474.109 158.55418 0 3764.8706 3.4940447
5850 16957.663 624.72623 0 3765.0342 10.739819
5900 19950.579 70.027987 0 3764.5796 4.6925057
5950 19759.601 105.38621 0 3764.5716 3.0958319
6000 19129.749 221.96406 0 3764.5102 -1.0612997
6050 16087.951 785.36134 0 3764.6115 -15.255986
6100 18851.976 272.98306 0 3764.0896 4.9341766
6150 19532.23 147.4113 0 3764.4909 1.3206073
6200 18051.604 421.79367 0 3764.6833 2.587863
6250 18922.77 259.81211 0 3764.0287 10.363589
6300 18402.504 356.81518 0 3764.6864 8.3589218
6350 19315.369 187.64457 0 3764.5647 1.0716382
6400 19700.59 116.50438 0 3764.7618 2.165408
6450 19596.362 135.79675 0 3764.7527 1.6466783
6500 20217.677 20.884953 0 3764.8993 -3.5893732
6550 18278.991 379.95981 0 3764.9582 7.0433091
6600 20142.999 34.761283 0 3764.9462 1.7083655
6650 20185.488 26.899017 0 3764.9524 -0.65741058
6700 17942.962 441.72909 0 3764.4999 -3.691039
6750 16435.681 720.9581 0 3764.6028 -9.4583249
6800 17825.95 463.58979 0 3764.6916 6.1557503
6850 19440.75 164.52796 0 3764.6669 -11.921703
6900 18824.905 278.4897 0 3764.5832 -1.4668322
6950 19069.14 233.25502 0 3764.5772 6.8149838
7000 18983.209 249.29193 0 3764.701 15.140158
7050 15623.103 872.33684 0 3765.5041 7.3268767
7100 20090.283 44.006184 0 3764.429 2.6959947
7150 15535.27 888.39683 0 3765.2987 -4.1285644
7200 19425.575 167.19079 0 3764.5195 4.9190857
7250 18684.497 304.24754 0 3764.3396 7.3927682
7300 17632.518 498.82765 0 3764.1087 5.1101854
7350 18969.793 251.66375 0 3764.5884 -3.7865508
7400 17700.626 486.89931 0 3764.7931 -8.8531288
7450 17897.361 450.31562 0 3764.6417 -3.6095062
7500 18795.228 284.03842 0 3764.6361 8.3567203
7550 18658.285 309.34015 0 3764.5781 0.4306691
7600 19230.039 203.5385 0 3764.6567 0.80253549
7650 19513.551 150.86999 0 3764.4906 0.32848159
7700 19494.849 154.28788 0 3764.4452 -4.2498631
7750 20011.058 58.832118 0 3764.5835 0.54896615
7800 19241.055 201.57548 0 3764.7338 -0.26200786
7850 19512.742 151.11436 0 3764.5851 2.7308876
7900 19688.007 118.68023 0 3764.6075 0.80454178
7950 16891.645 636.56823 0 3764.6507 -25.839253
8000 19425.572 167.33746 0 3764.6657 -2.8744687
8050 19444.916 163.57779 0 3764.4882 8.5388183
8100 19540.338 145.77731 0 3764.3585 5.5606379
8150 17997.991 429.85951 0 3762.8208 20.179487
8200 19463.886 159.50302 0 3763.9264 0.19577123
8250 19517.733 149.53457 0 3763.9295 2.3294314
8300 19236.221 201.66041 0 3763.9236 5.8204747
8350 18662.608 308.25544 0 3764.2939 5.4422482
8400 19030.046 239.38211 0 3763.4647 3.7940188
8450 18058.148 419.70672 0 3763.8081 4.4010713
8500 16866.001 641.00564 0 3764.3392 -19.894815
8550 19484.364 155.35821 0 3763.5737 4.2635496
8600 18562.912 326.16323 0 3763.7395 11.288271
8650 19256.188 197.67578 0 3763.6365 -4.1872666
8700 19653.945 124.27148 0 3763.8909 -7.4888761
8750 19590.834 136.12748 0 3764.0596 1.0605539
8800 19065.424 233.46882 0 3764.1029 1.8432113
8850 18961.297 252.69734 0 3764.0486 6.7414134
8900 19879.711 82.777822 0 3764.2058 0.12631864
8950 18689.712 302.80546 0 3763.8632 5.1584036
9000 19114.403 224.23511 0 3763.9393 -4.5856366
9050 17626.3 500.49518 0 3764.6248 -3.9436947
9100 18552.501 328.86032 0 3764.5087 -0.32810034
9150 15039.846 979.12961 0 3764.2862 16.571104
9200 19146.923 218.64681 0 3764.3733 -4.6264398
9250 17606.161 503.14852 0 3763.5487 13.13675
9300 18002.328 430.47362 0 3764.2381 4.9326117
9350 19980.452 64.168644 0 3764.2524 -5.6111349
9400 18953.798 254.44926 0 3764.4118 2.3662302
9450 17151.075 588.59472 0 3764.7197 4.3116983
9500 19128.858 221.38199 0 3763.763 3.6641306
9550 18217.322 390.53199 0 3764.1101 1.8537154
9600 19094.478 227.98925 0 3764.0038 3.972665
9650 19577.649 138.55507 0 3764.0456 4.0408247
9700 19331.361 184.31942 0 3764.2011 -4.7996733
9750 18999.798 245.87295 0 3764.3541 -0.26741334
9800 18987.181 248.37105 0 3764.5157 6.1717595
9850 20094.73 43.013036 0 3764.2593 -8.9770288
9900 18988.815 247.63984 0 3764.087 -6.3990966
9950 18290.808 377.34967 0 3764.5363 7.7453525
10000 19558.326 142.47047 0 3764.3828 3.4110829
Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms
Performance: 24418.438 tau/day, 2826.208 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 | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00
Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63
Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05
Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19
Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14
Other | | 0.0352 | | | 0.99
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 17.5 ave 37 max 1 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 154.25 ave 393 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 617
Ave neighs/atom = 7.61728
Neighbor list builds = 993
Dangerous builds = 948
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

340
examples/rigid/log.20Apr18.rigid.property.g++.1 Normal file
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@ -0,0 +1,340 @@
LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.046 | 4.046 | 4.046 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550102 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms
Performance: 613990.898 tau/day, 71063.761 timesteps/s
97.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73
Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47
Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55
Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77
Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09
Other | | 0.006187 | | | 4.40
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
atom_style atomic
atom_modify map array
pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
# assemble bodies from per-atom custom integer property bodies
fix 1 all rigid custom i_bodies
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 4.017 | 4.111 | 4.392 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.135501 0 5269.5101 11.407245
9800 16738.512 -0.011620329 0 5269.5201 11.394973
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms
Performance: 418940.303 tau/day, 48488.461 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 | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03
Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20
Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62
Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50
Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53
Other | | 0.01055 | | | 5.11
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
update every 1 steps, delay 0 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 = 45 45 45
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/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106
2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134
3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861
3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037
3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321
3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736
3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532
3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716
3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599
3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767
3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832
3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184
4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721
4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459
4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681
4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067
4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185
4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378
4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102
4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176
4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431
4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736
5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324
Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms
Performance: 320596.735 tau/day, 742.122 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 | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81
Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95
Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64
Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38
Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06
Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58
Other | | 0.1735 | | | 2.57
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1352 ave 1352 max 1352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5257 ave 5257 max 5257 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5257
Ave neighs/atom = 0.93875
Ave special neighs/atom = 0.571429
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554
5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085
5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108
5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935
5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084
5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628
5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843
5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286
5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054
5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358
6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488
Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms
Performance: 306205.780 tau/day, 708.810 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 | 0.149 | 0.149 | 0.149 | 0.0 | 10.56
Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82
Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19
Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30
Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06
Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60
Other | | 0.03491 | | | 2.47
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1347 ave 1347 max 1347 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5592 ave 5592 max 5592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5592
Ave neighs/atom = 0.998571
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429
6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278
6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897
6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564
6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155
6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487
6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719
6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031
6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821
6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742
7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771
Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms
Performance: 299769.942 tau/day, 693.912 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 | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36
Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71
Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94
Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29
Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06
Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20
Other | | 0.03506 | | | 2.43
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5541 ave 5541 max 5541 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5541
Ave neighs/atom = 0.989464
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521
7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973
7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938
7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059
7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524
7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326
7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195
7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457
7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129
7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936
8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995
Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms
Performance: 139749.554 tau/day, 323.494 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 | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40
Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56
Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35
Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35
Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03
Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92
Other | | 0.04324 | | | 1.40
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2922 ave 2922 max 2922 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24639 ave 24639 max 24639 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24639
Ave neighs/atom = 4.39982
Ave special neighs/atom = 0.571429
Neighbor list builds = 335
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368
8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024
8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975
8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871
8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782
8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368
8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773
8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679
8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819
8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357
9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504
Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms
Performance: 141361.930 tau/day, 327.227 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 | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76
Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63
Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25
Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87
Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03
Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20
Other | | 0.03837 | | | 1.26
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3326 ave 3326 max 3326 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31301 ave 31301 max 31301 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31301
Ave neighs/atom = 5.58946
Ave special neighs/atom = 0.571429
Neighbor list builds = 168
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579
9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042
9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329
9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893
9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244
9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087
9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896
9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362
9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545
9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207
10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467
Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms
Performance: 133348.758 tau/day, 308.678 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 | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00
Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48
Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10
Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90
Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02
Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30
Other | | 0.03849 | | | 1.19
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3617 ave 3617 max 3617 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35834 ave 35834 max 35834 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35834
Ave neighs/atom = 6.39893
Ave special neighs/atom = 0.571429
Neighbor list builds = 162
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513
10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871
10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525
10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543
10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677
10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067
10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719
10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951
10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606
10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411
11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472
Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms
Performance: 126326.531 tau/day, 292.423 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 | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96
Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36
Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57
Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88
Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02
Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07
Other | | 0.03903 | | | 1.14
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3805 ave 3805 max 3805 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40038 ave 40038 max 40038 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40038
Ave neighs/atom = 7.14964
Ave special neighs/atom = 0.571429
Neighbor list builds = 162
Dangerous builds = 0
Total wall time: 0:00:22

458
examples/rigid/log.20Apr18.rigid.tnr.g++.4 Normal file
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LAMMPS (20 Apr 2018)
using 1 OpenMP thread(s) per MPI task
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule/intra rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
update every 1 steps, delay 0 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 = 45 45 45
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/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028
2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539
2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112
2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357
2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412
2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892
3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658
3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485
3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783
3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048
3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724
3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433
3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225
3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455
3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624
3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689
4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626
4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172
4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746
4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924
4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638
4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334
4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263
4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225
4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449
4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056
5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771
Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms
Performance: 624133.913 tau/day, 1444.754 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85
Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91
Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76
Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58
Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10
Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02
Other | | 0.2 | | | 5.78
Nlocal: 1400 ave 1844 max 907 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 642 ave 714 max 581 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 1307.25 ave 1883 max 682 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 5229
Ave neighs/atom = 0.93375
Ave special neighs/atom = 0.571429
Neighbor list builds = 762
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215
5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298
5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911
5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068
5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373
5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707
5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387
5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341
5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223
5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198
6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689
Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms
Performance: 544612.641 tau/day, 1260.677 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55
Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66
Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30
Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11
Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09
Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66
Other | | 0.04459 | | | 5.62
Nlocal: 1400 ave 1844 max 884 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 713.5 ave 818 max 656 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 1315 ave 1956 max 573 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 5260
Ave neighs/atom = 0.939286
Ave special neighs/atom = 0.571429
Neighbor list builds = 156
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779
6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027
6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881
6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499
6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801
6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659
6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155
6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075
6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066
6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381
7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375
Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms
Performance: 531376.713 tau/day, 1230.039 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74
Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62
Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33
Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10
Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09
Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04
Other | | 0.04134 | | | 5.09
Nlocal: 1400 ave 1861 max 953 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 732.5 ave 799 max 634 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 1478.5 ave 2087 max 852 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5914
Ave neighs/atom = 1.05607
Ave special neighs/atom = 0.571429
Neighbor list builds = 154
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619
7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475
7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823
7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808
7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154
7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934
7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266
7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104
7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242
7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921
8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435
Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms
Performance: 292430.022 tau/day, 676.921 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82
Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35
Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30
Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68
Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03
Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73
Other | | 0.04563 | | | 3.09
Nlocal: 1400 ave 1711 max 1074 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1617 ave 1748 max 1514 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 6221.75 ave 8875 max 3829 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 24887
Ave neighs/atom = 4.44411
Ave special neighs/atom = 0.571429
Neighbor list builds = 340
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531
8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895
8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249
8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714
8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747
8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867
8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873
8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702
8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987
8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801
9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686
Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms
Performance: 304989.819 tau/day, 705.995 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25
Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42
Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36
Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21
Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04
Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92
Other | | 0.03963 | | | 2.80
Nlocal: 1400 ave 1641 max 1120 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 1593.5 ave 1674 max 1480 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 7766.25 ave 10004 max 5618 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 31065
Ave neighs/atom = 5.54732
Ave special neighs/atom = 0.571429
Neighbor list builds = 168
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595
9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716
9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967
9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325
9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319
9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422
9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125
9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226
9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283
9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026
10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892
Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms
Performance: 293069.938 tau/day, 678.403 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 | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07
Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37
Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66
Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03
Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04
Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18
Other | | 0.0391 | | | 2.65
Nlocal: 1400 ave 1629 max 1159 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 1760.25 ave 1871 max 1635 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 9467.75 ave 11967 max 6712 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 37871
Ave neighs/atom = 6.76268
Ave special neighs/atom = 0.571429
Neighbor list builds = 163
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506
10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812
10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461
10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255
10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884
10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428
10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401
10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703
10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507
10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896
11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759
Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms
Performance: 287222.965 tau/day, 664.868 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 | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15
Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36
Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36
Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19
Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03
Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41
Other | | 0.0375 | | | 2.49
Nlocal: 1400 ave 1605 max 1229 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 1859 ave 1964 max 1718 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 10208.2 ave 13091 max 7670 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 40833
Ave neighs/atom = 7.29161
Ave special neighs/atom = 0.571429
Neighbor list builds = 160
Dangerous builds = 0
Total wall time: 0:00:10

332
examples/rigid/log.5Oct16.rigid.poems.g++.1
View File

@ -1,332 +0,0 @@
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 2.96781 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699149
1200 21815.003 45.317414 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773952
1400 21485.029 99.812921 0 3680.6511 -16.185473
1450 21771.107 52.15961 0 3680.6775 -2.4756673
1500 21520.948 93.503927 0 3680.3286 2.1023576
1550 21351.418 121.68137 0 3680.2511 5.5159947
1600 20778.805 216.92177 0 3680.0559 15.089188
1650 21477.638 100.21836 0 3679.8247 -1.1045746
1700 18501.339 596.47914 0 3680.0357 -15.679679
1750 18563.642 587.34785 0 3681.2882 33.532209
1800 19110.185 494.8234 0 3679.8543 18.024046
1850 21364.191 119.23545 0 3679.9339 2.5291103
1900 20146.626 322.14867 0 3679.9197 5.7313218
1950 20692.672 231.25325 0 3680.0319 4.2977763
2000 20943.904 189.11235 0 3679.7629 -22.645121
2050 19668.057 401.82994 0 3679.8394 3.6251916
2100 20280.442 299.76155 0 3679.8353 7.4807949
2150 19181.86 483.522 0 3680.4987 22.620507
2200 21300.161 130.70534 0 3680.7322 4.7102665
2250 20486.943 266.63931 0 3681.1299 -8.6456512
2300 18653.122 572.24819 0 3681.1018 -5.2637122
2350 21513.523 95.614901 0 3681.2021 -9.3621767
2400 21466.272 103.56446 0 3681.2765 -29.561368
2450 20100.105 332.27123 0 3682.2887 35.744287
2500 20764.395 221.6677 0 3682.4001 -12.468906
2550 20435.699 276.31055 0 3682.2603 -22.413697
2600 21466.467 104.53618 0 3682.2807 -10.078508
2650 20814.737 213.23892 0 3682.3617 5.1390411
2700 18565.761 588.3578 0 3682.6513 22.27664
2750 20772.36 220.1607 0 3682.2206 -7.9448198
2800 21018.563 179.10058 0 3682.1945 -7.0717829
2850 16789.412 884.21472 0 3682.4501 33.279015
2900 19304.363 464.75282 0 3682.1466 7.947554
2950 20513.758 263.07578 0 3682.0355 2.2361434
3000 20617.309 245.95251 0 3682.1706 -0.75213689
3050 18567.52 587.90473 0 3682.4914 -4.0112006
3100 18696.577 566.20617 0 3682.3023 -1.4814167
3150 19864.606 371.56078 0 3682.3284 8.9362836
3200 18902.643 532.04614 0 3682.4867 0.76630303
3250 21110.454 163.86212 0 3682.271 -1.6253894
3300 19369.939 454.05833 0 3682.3816 4.9066544
3350 19082.603 501.69905 0 3682.133 3.5982292
3400 19527.779 426.918 0 3681.5478 6.9612143
3450 19892.953 366.19989 0 3681.6921 3.0050426
3500 19708.981 396.84552 0 3681.6756 7.0757635
3550 20256.096 306.23937 0 3682.2554 -1.752138
3600 21289.889 133.93823 0 3682.253 -3.7462615
3650 18333.877 627.18028 0 3682.8264 -15.276791
3700 19829.133 377.33753 0 3682.1931 -6.269648
3750 20771.635 220.07171 0 3682.0109 -28.479036
3800 18373.813 619.79253 0 3682.0947 29.594781
3850 19320.99 461.92786 0 3682.0928 -5.3212101
3900 16119.825 995.68064 0 3682.3182 -8.4683118
3950 15556.948 1091.3655 0 3684.1902 20.98273
4000 20000.464 348.24891 0 3681.6596 7.1589745
4050 18870.219 536.59924 0 3681.6358 -3.7997025
4100 19889.518 367.49253 0 3682.4122 -14.091266
4150 15789.623 1051.3399 0 3682.9438 -4.4152389
4200 20548.889 256.83493 0 3681.6498 0.92234153
4250 20681.925 235.46113 0 3682.4487 -11.515773
4300 19330.404 460.80975 0 3682.5437 -22.351775
4350 19369.443 453.35405 0 3681.5945 29.418242
4400 20762.165 222.24133 0 3682.6021 2.6627047
4450 19984.657 350.71294 0 3681.4891 28.88731
4500 21167.58 154.25344 0 3682.1834 -3.0784322
4550 18133.576 660.73671 0 3682.9995 2.5305835
4600 19935.069 360.36826 0 3682.8798 2.4575034
4650 21413.76 113.86464 0 3682.8246 -5.1271547
4700 21716.333 63.609419 0 3682.9982 -2.4708049
4750 21352.947 124.36961 0 3683.1941 -0.29026265
4800 19043.788 508.8617 0 3682.8264 14.797006
4850 20516.121 263.78758 0 3683.1411 7.1348281
4900 20624.5 245.81827 0 3683.235 0.34708051
4950 20317.197 296.68937 0 3682.8889 -0.55065946
5000 18346.865 625.37246 0 3683.1832 7.3371413
5050 18867.53 538.49153 0 3683.0799 1.9249866
5100 18790.276 551.17224 0 3682.885 2.2333017
5150 20241.365 311.84683 0 3685.4076 -3.998004
5200 17685.058 739.76418 0 3687.2739 3.2835025
5250 18496.626 604.58166 0 3687.3526 -10.185776
5300 18420.042 617.82026 0 3687.8273 -16.392458
5350 18767.338 559.0349 0 3686.9246 4.5320767
5400 20423.245 284.90517 0 3688.7794 -8.6356656
5450 21080.398 176.18494 0 3689.5846 -16.450038
5500 16684.424 909.12643 0 3689.8637 49.94555
5550 20132.31 335.03663 0 3690.4216 -16.018038
5600 20430.923 285.17562 0 3690.3295 -5.0773675
5650 20479.943 276.55962 0 3689.8834 5.4334564
5700 20061.532 345.95553 0 3689.5441 -16.230658
5750 20523.759 268.92217 0 3689.5487 -4.4128812
5800 18900.356 537.65462 0 3687.7139 13.605549
5850 20280.502 310.27193 0 3690.3556 -4.7884959
5900 19050.26 515.66087 0 3690.7042 7.8864722
5950 19566.917 430.2997 0 3691.4525 31.715268
6000 18878.118 544.75449 0 3691.1076 -4.2415329
6050 19308.682 471.70734 0 3689.821 -10.561614
6100 18776.194 560.04764 0 3689.4133 -7.7286747
6150 21475.064 110.1508 0 3689.3281 -3.6506391
6200 19975 360.82675 0 3689.9934 10.282021
6250 21396.341 123.5341 0 3689.5909 -5.7215163
6300 18533.423 600.87422 0 3689.778 15.408027
6350 20653.152 247.19253 0 3689.3846 8.5607784
6400 19716.537 403.41487 0 3689.5044 13.165575
6450 21120.66 168.79838 0 3688.9084 -0.50382728
6500 19700.345 404.7155 0 3688.1064 13.941375
6550 10818.393 1892.037 0 3695.1025 38.423155
6600 18684.478 574.84755 0 3688.9273 5.9176985
6650 19219.732 486.04269 0 3689.3314 18.287659
6700 20058.587 344.88255 0 3687.9804 6.5372086
6750 21279.318 142.77333 0 3689.3264 2.498188
6800 20671.545 244.25024 0 3689.5078 -4.1356416
6850 21203.598 155.82001 0 3689.753 -0.0083061182
6900 21699.344 73.301497 0 3689.8588 -8.0309898
6950 20951.212 197.19403 0 3689.0627 0.76668303
7000 20166.275 329.02869 0 3690.0746 2.0083318
7050 21554.944 97.465792 0 3689.9564 -3.2420086
7100 20817.494 220.25476 0 3689.8372 0.17206182
7150 21481.11 109.84029 0 3690.0253 -3.6814741
7200 21266.824 145.53099 0 3690.0016 -2.060543
7250 19434.684 450.81331 0 3689.9273 9.4822765
7300 21246.525 148.96573 0 3690.0532 3.3208839
7350 19749.269 398.60049 0 3690.1454 1.0929662
7400 20354.792 297.70261 0 3690.168 1.547159
7450 19996.859 357.16723 0 3689.977 -0.68412025
7500 20179.628 326.53243 0 3689.8038 -2.4805507
7550 18765.184 561.65039 0 3689.1811 -1.7976428
7600 19457.496 447.04428 0 3689.9603 -1.9055522
7650 18206.823 655.57276 0 3690.0433 1.2797964
7700 19152.344 497.77422 0 3689.8315 18.145069
7750 21387.484 125.48654 0 3690.0673 -2.9915772
7800 18127.052 668.61425 0 3689.7896 9.044869
7850 21419.557 120.08889 0 3690.015 6.2651717
7900 21817.182 53.739819 0 3689.9368 -4.2387416
7950 18215.195 654.15494 0 3690.0208 -54.628049
8000 21523.503 102.58018 0 3689.8307 -4.84236
8050 20720.799 236.28689 0 3689.7535 -9.3725225
8100 21196.483 157.3232 0 3690.0704 -7.7222497
8150 20869.667 211.65308 0 3689.9309 -6.8438295
8200 17790.052 725.72497 0 3690.7336 -25.697688
8250 19634.94 417.71929 0 3690.2094 8.861604
8300 19135.784 500.92443 0 3690.2218 -3.1245167
8350 20191.718 324.93312 0 3690.2195 6.5736107
8400 20695.239 241.02378 0 3690.2302 -14.592221
8450 21793.857 57.609525 0 3689.9191 -11.509747
8500 21271.088 144.43102 0 3689.6124 -0.091587085
8550 20064.337 345.21754 0 3689.2737 9.5058471
8600 20282.86 308.2307 0 3688.7074 2.265529
8650 21223.055 151.24306 0 3688.419 1.7296834
8700 18875.342 542.42055 0 3688.3108 6.367148
8750 20922.65 201.55122 0 3688.6595 3.4208578
8800 21406.54 120.8539 0 3688.6106 1.8253729
8850 19868.524 377.05623 0 3688.477 16.327796
8900 20025.322 348.94892 0 3686.5025 17.063406
8950 21224.374 151.3567 0 3688.7524 -0.11028753
9000 21318.309 135.862 0 3688.9135 -0.50826819
9050 17538.618 768.00136 0 3691.1043 37.978645
9100 21247.861 147.84641 0 3689.1566 -6.7773259
9150 18455.677 613.08767 0 3689.0339 -3.4844751
9200 19486.859 441.03829 0 3688.8482 -18.602827
9250 21774.926 59.710446 0 3688.8648 -13.379919
9300 17628.877 750.72321 0 3688.8694 27.797974
9350 19827.334 383.85708 0 3688.4128 6.5459021
9400 20020.126 351.61742 0 3688.3051 -14.332562
9450 21596.338 88.904175 0 3688.2939 1.5779716
9500 18981.418 524.60141 0 3688.1711 5.4352409
9550 18652.616 579.05144 0 3687.8208 25.600729
9600 21198.037 155.23097 0 3688.2371 -3.3586596
9650 19958.317 361.32544 0 3687.7115 4.2910178
9700 19129.101 499.5993 0 3687.7828 13.267102
9750 21913.967 35.689587 0 3688.0174 -7.3222905
9800 21314.694 135.43794 0 3687.8869 -9.5613518
9850 20899.743 204.82802 0 3688.1185 -2.6321428
9900 20288.244 306.5013 0 3687.8753 3.6196618
9950 19271.015 475.88527 0 3687.7211 -1.8196764
10000 21122.24 167.82714 0 3688.2005 -3.8464842
Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms
Performance: 23575.670 tau/day, 2728.665 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26
Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70
Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24
Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04
Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56
Other | | 0.007194 | | | 0.20
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 744 ave 744 max 744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 744
Ave neighs/atom = 9.18519
Neighbor list builds = 992
Dangerous builds = 941
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

332
examples/rigid/log.5Oct16.rigid.poems.g++.4
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@ -1,332 +0,0 @@
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 2.94053 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384276
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.8669916
1200 21815.003 45.317417 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36504 0 3680.8286 6.0538619
1350 20558.972 254.3648 0 3680.8601 -3.6773987
1400 21485.029 99.812949 0 3680.6511 -16.185471
1450 21771.108 52.15959 0 3680.6775 -2.4756681
1500 21520.948 93.503949 0 3680.3286 2.1023578
1550 21351.418 121.6814 0 3680.2511 5.5159978
1600 20778.805 216.92171 0 3680.0559 15.089182
1650 21477.639 100.2182 0 3679.8247 -1.1045944
1700 18501.343 596.47853 0 3680.0357 -15.67963
1750 18563.643 587.34767 0 3681.2882 33.532167
1800 19110.19 494.82264 0 3679.8543 18.024034
1850 21364.196 119.23454 0 3679.9339 2.5291491
1900 20146.643 322.14595 0 3679.9197 5.731152
1950 20692.67 231.25357 0 3680.0319 4.2977641
2000 20943.904 189.11223 0 3679.763 -22.645645
2050 19668.152 401.81407 0 3679.8394 3.6255896
2100 20280.572 299.73976 0 3679.8351 7.4809355
2150 19182.121 483.47905 0 3680.4992 22.615309
2200 21299.76 130.77281 0 3680.7327 4.7114154
2250 20487.784 266.4995 0 3681.1302 -8.6406776
2300 18655.125 571.91487 0 3681.1023 -5.2671669
2350 21512.614 95.766913 0 3681.2025 -9.3523428
2400 21467.773 103.31519 0 3681.2773 -29.600307
2450 20096.937 332.80159 0 3682.2911 35.890912
2500 20761.446 222.16118 0 3682.4022 -12.528127
2550 20409.6 280.67234 0 3682.2723 -22.277373
2600 21469.964 103.95529 0 3682.2826 -10.038267
2650 20708.138 231.00516 0 3682.3615 5.3659502
2700 18584.743 585.07862 0 3682.5357 21.785261
2750 20503.019 264.91491 0 3682.0847 -4.5583917
2800 20584.075 251.44664 0 3682.1258 -6.5084595
2850 17277.076 802.33356 0 3681.8462 15.519513
2900 19392.956 449.92915 0 3682.0885 -4.3829957
2950 18371.786 620.29835 0 3682.2626 7.2117592
3000 20412.015 280.25302 0 3682.2555 0.32492606
3050 20858.248 205.65269 0 3682.0273 4.5055715
3100 21561.094 88.438447 0 3681.9541 -3.7523733
3150 15471.278 1103.4497 0 3681.9961 -14.576367
3200 15386.973 1117.8815 0 3682.377 15.051163
3250 19741.037 392.04755 0 3682.2204 -2.6610995
3300 20870.191 203.58229 0 3681.9475 -4.7795545
3350 16648.228 907.66571 0 3682.3704 -8.9242511
3400 20104.016 331.58603 0 3682.2554 6.4783858
3450 21421.316 112.28228 0 3682.5015 -8.3484987
3500 19284.533 467.80739 0 3681.8962 -12.835452
3550 20160.125 322.4476 0 3682.4684 1.6574827
3600 16682.415 902.73752 0 3683.14 22.383296
3650 16762.19 890.14636 0 3683.8446 16.119412
3700 17858.568 707.37212 0 3683.8 -1.6582504
3750 20029.881 345.15986 0 3683.4733 -3.1415889
3800 20734 227.99158 0 3683.6582 -7.9580418
3850 20741.089 226.39408 0 3683.2423 8.3055765
3900 18671.251 571.42296 0 3683.2981 -3.7468858
3950 19547.209 423.14256 0 3681.0108 5.8312279
4000 19739.799 393.58799 0 3683.5544 18.604884
4050 20014.121 347.8176 0 3683.5044 9.93387
4100 20503.654 266.08691 0 3683.3626 8.1304118
4150 18309.702 632.29807 0 3683.9151 -0.0021480359
4200 20509.423 265.60353 0 3683.8408 -2.1658857
4250 21805.541 50.325935 0 3684.5828 1.082842
4300 21420.551 114.90431 0 3684.9962 -1.7985998
4350 20256.928 308.74187 0 3684.8966 -11.669472
4400 21633.488 79.629274 0 3685.2106 -0.96131785
4450 20793.327 219.66955 0 3685.2241 1.3752349
4500 18719.484 564.86754 0 3684.7816 2.6308699
4550 20966.335 190.68308 0 3685.0722 -18.587627
4600 19428.962 446.59618 0 3684.7565 -4.4051672
4650 18408.956 616.85009 0 3685.0095 2.777272
4700 19215.779 482.57562 0 3685.2054 19.441016
4750 20155.927 326.13401 0 3685.4553 6.1734993
4800 20918.085 199.31832 0 3685.6659 3.4407437
4850 20236.958 312.07276 0 3684.899 3.2612893
4900 21419.89 115.36879 0 3685.3505 -4.675951
4950 19707.901 401.14828 0 3685.7985 -10.730734
5000 19407.201 450.64394 0 3685.1775 17.518981
5050 21527.598 97.655186 0 3685.5882 -9.2294707
5100 21581.933 88.595517 0 3685.5843 -20.669485
5150 21161.214 158.48503 0 3685.3541 -2.7587502
5200 21166.679 157.24762 0 3685.0275 -18.180044
5250 20909.576 200.23507 0 3685.1644 -16.617303
5300 21911.746 33.236563 0 3685.1942 -5.8313967
5350 20857.303 208.87453 0 3685.0916 12.176312
5400 20958.96 191.96694 0 3685.1269 3.6116429
5450 20433.179 279.61178 0 3685.1415 13.324529
5500 19604.675 416.88499 0 3684.3308 21.536484
5550 18171.145 655.92915 0 3684.4534 -9.2269804
5600 19799.907 385.12116 0 3685.1056 22.202165
5650 19711.882 399.30581 0 3684.6194 15.93063
5700 17908.833 699.52405 0 3684.3295 0.35530356
5750 18606.518 583.538 0 3684.6243 -4.4540843
5800 21814.053 48.974627 0 3684.6501 -1.5206358
5850 18029.107 679.9357 0 3684.7868 12.137677
5900 21090.739 169.64502 0 3684.7682 -1.5051545
5950 21086.26 170.29075 0 3684.6674 -2.8164474
6000 21285.771 136.95608 0 3684.5846 -26.582739
6050 21203.994 150.87822 0 3684.8772 -2.6617226
6100 21481.553 104.57796 0 3684.8368 -16.524974
6150 20354.4 292.57675 0 3684.9767 2.7960207
6200 21326.591 130.75243 0 3685.1843 -1.5929194
6250 21505.087 101.07817 0 3685.2593 -3.7821931
6300 21296.273 135.6593 0 3685.0382 -0.55635908
6350 21295.389 135.86485 0 3685.0964 5.6614093
6400 16552.242 926.02655 0 3684.7336 14.177218
6450 20148.951 327.1151 0 3685.2736 7.4561085
6500 20962.151 191.79415 0 3685.486 -4.5436711
6550 21710.328 67.433972 0 3685.8219 -5.7678572
6600 20698.571 234.79099 0 3684.5528 -2.1984068
6650 17892.287 704.05484 0 3686.1026 11.525836
6700 21272.999 141.26589 0 3686.7657 0.44088069
6750 19558.993 426.46448 0 3686.2966 -16.907401
6800 20350.247 295.23951 0 3686.9474 1.1284348
6850 18665.05 573.5326 0 3684.3742 17.088712
6900 19769.199 392.1551 0 3687.0216 6.7562425
6950 19439.159 446.99138 0 3686.8512 -6.0105763
7000 19379.907 456.53471 0 3686.5192 -9.0505095
7050 19983.754 356.02523 0 3686.651 -5.6274314
7100 19867.737 375.47627 0 3686.7658 17.315482
7150 19258.794 477.47344 0 3687.2724 14.316676
7200 21282.428 139.96051 0 3687.0318 -0.77043459
7250 19828.603 381.98919 0 3686.7564 6.5142869
7300 20574.582 257.8245 0 3686.9215 -3.6547118
7350 21613.467 84.771568 0 3687.0161 -7.5188826
7400 21817.009 50.844944 0 3687.0131 -14.888864
7450 14937.538 1197.4257 0 3687.0154 1.7540499
7500 18326.914 632.40374 0 3686.8894 8.3397357
7550 13611.007 1418.4727 0 3686.9739 -19.379482
7600 19173.985 491.9482 0 3687.6123 17.229001
7650 16911.504 867.33649 0 3685.9204 -21.042834
7700 21752.116 61.143705 0 3686.4963 -10.344487
7750 20208.337 318.26355 0 3686.3197 13.385814
7800 21649.909 77.950987 0 3686.2692 -1.7911084
7850 20139.64 329.50319 0 3686.1098 -5.5805093
7900 21355.026 126.7642 0 3685.9352 -7.7062172
7950 21336.178 129.88925 0 3685.9188 -2.059298
8000 21047.596 177.71546 0 3685.6482 0.37963466
8050 19217.351 482.62331 0 3685.5152 6.5582595
8100 20499.057 268.7173 0 3685.2268 -1.1959737
8150 21494.301 102.83829 0 3685.2219 -1.6427647
8200 20074.928 339.19817 0 3685.0195 6.285123
8250 17335.157 793.47566 0 3682.6685 22.877381
8300 17340.544 794.62619 0 3684.7168 3.9147755
8350 20529.345 262.51162 0 3684.0691 4.031768
8400 18884.747 537.47827 0 3684.9361 22.853404
8450 20341.86 293.10484 0 3683.4148 0.33856656
8500 19300.282 467.58127 0 3684.2949 12.35507
8550 21631.936 78.254534 0 3683.5772 -10.992959
8600 20204.913 316.83233 0 3684.3178 20.74228
8650 21018.189 181.32054 0 3684.352 1.8412068
8700 20161.304 323.97907 0 3684.1964 -2.646629
8750 19081.79 504.00155 0 3684.2998 -10.088053
8800 20834.489 211.76247 0 3684.1773 14.896336
8850 20929.355 196.18335 0 3684.4092 -1.2602398
8900 21491.074 102.47788 0 3684.3235 -1.4696758
8950 20474.735 271.69461 0 3684.1504 -6.9489258
9000 21128.641 162.40732 0 3683.8474 -7.7928168
9050 18421.801 614.46442 0 3684.7646 24.40313
9100 19301.292 466.98873 0 3683.8707 4.4687046
9150 21575.705 88.213763 0 3684.1646 -0.94696984
9200 20004.776 350.05448 0 3684.1838 -7.3466605
9250 21384.079 120.14472 0 3684.1578 -8.3773844
9300 21980.599 20.702393 0 3684.1356 -12.666293
9350 21686.606 69.517984 0 3683.9524 -8.8366533
9400 20732.704 228.46247 0 3683.9131 -6.4080307
9450 19798.859 384.34696 0 3684.1568 7.6198484
9500 20270.695 305.22664 0 3683.6758 1.5862486
9550 16496.156 935.28481 0 3684.6441 15.001468
9600 20642.429 241.08853 0 3681.4934 -9.2159382
9650 21292.587 135.4474 0 3684.2119 -0.54770976
9700 18888.158 536.60518 0 3684.6315 5.3236926
9750 18750.018 559.35922 0 3684.3623 -9.9424949
9800 20544.772 259.71076 0 3683.8394 8.732202
9850 16698.125 901.90076 0 3684.9216 9.9553329
9900 21450.963 109.58687 0 3684.7474 -4.8001999
9950 20664.461 240.66995 0 3684.7468 -3.4840781
10000 18951.367 526.45428 0 3685.0155 21.512727
Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms
Performance: 22205.346 tau/day, 2570.063 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02
Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70
Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52
Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14
Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96
Other | | 0.02605 | | | 0.67
Nlocal: 20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 95 max 14 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 249.25 ave 997 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 997
Ave neighs/atom = 12.3086
Neighbor list builds = 993
Dangerous builds = 943
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

336
examples/rigid/log.5Oct16.rigid.poems2.g++.1
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@ -1,336 +0,0 @@
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 3.53031 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15175 0 3764.0939 -1.6134531
1550 18147.996 404.12677 0 3764.8668 8.4194779
1600 18615.043 317.42467 0 3764.6548 -2.3288934
1650 20120.654 38.887913 0 3764.935 -8.7620277
1700 19450.907 162.98272 0 3765.0025 2.3254731
1750 19374.632 177.37966 0 3765.2744 8.9328774
1800 19424.404 167.93966 0 3765.0514 0.081230261
1850 17936.249 442.84231 0 3764.3699 6.6010636
1900 19982.595 64.406198 0 3764.8868 -2.9529813
1950 16215.852 761.91287 0 3764.8485 13.994708
2000 18584.422 322.12049 0 3763.68 7.1654003
2050 20107.965 41.025754 0 3764.723 -0.3109069
2100 20002.333 60.593017 0 3764.7288 -6.7919784
2150 16949.762 626.59623 0 3765.441 3.508941
2200 20010.953 58.808279 0 3764.5403 -10.862172
2250 18982.73 247.00892 0 3762.3292 -0.53807815
2300 18401.298 354.87973 0 3762.5274 1.0920554
2350 19390.524 172.9415 0 3763.7793 -3.3524932
2400 16080.801 786.38838 0 3764.3146 -16.200514
2450 18870.412 268.74976 0 3763.2705 11.197736
2500 19688.29 117.58223 0 3763.5618 4.382644
2550 18870.825 268.78678 0 3763.384 -5.6623656
2600 17019.35 611.70808 0 3763.4395 6.3109641
2650 18753.285 291.0596 0 3763.8902 2.4120296
2700 19742.456 107.20901 0 3763.2193 -0.33061303
2750 19522.438 148.16759 0 3763.4339 -1.6254851
2800 18304.801 372.55152 0 3762.3295 22.6368
2850 18465.36 343.48495 0 3762.9961 4.4169272
2900 20151.999 31.372926 0 3763.2245 1.2013699
2950 15498.143 892.80071 0 3762.8272 13.263724
3000 18728.301 294.65113 0 3762.855 8.1897838
3050 18538.466 330.25223 0 3763.3015 8.5865739
3100 19081.409 229.5907 0 3763.1849 -4.8573813
3150 18498.802 337.11548 0 3762.8195 1.0555321
3200 19925.897 73.358029 0 3763.339 -7.7325108
3250 19780.108 100.23785 0 3763.2209 -5.5974972
3300 19221.043 203.82387 0 3763.2763 4.2703251
3350 19025.292 240.11329 0 3763.3156 5.7708328
3400 18153.696 401.52086 0 3763.3164 21.076943
3450 18611.375 316.50396 0 3763.0548 -3.5484945
3500 19931.319 71.969274 0 3762.9543 1.8764978
3550 19747.562 106.05439 0 3763.0103 -2.5506186
3600 18491.39 338.4134 0 3762.7449 -4.0527808
3650 19757.998 104.19207 0 3763.0806 1.4865598
3700 20108.003 39.345514 0 3763.0498 0.062827129
3750 19222.505 203.28065 0 3763.0039 0.33719277
3800 19286.383 191.08831 0 3762.6406 -0.1826802
3850 19450.083 161.09138 0 3762.9587 -0.2708263
3900 18002.304 429.25655 0 3763.0166 -4.6832439
3950 17186.829 582.26502 0 3765.0111 55.816834
4000 16826.434 645.84974 0 3761.856 19.675962
4050 19227.526 202.18151 0 3762.8344 -0.2596098
4100 19908.792 76.084531 0 3762.8978 -2.796813
4150 17821.329 462.63065 0 3762.8768 13.069155
4200 19917.133 74.574998 0 3762.9329 -6.4181155
4250 19012.618 241.96787 0 3762.823 4.0847974
4300 19077.34 229.98133 0 3762.8221 4.324323
4350 19361.128 177.47406 0 3762.8681 -7.377974
4400 18565.044 324.95107 0 3762.9223 2.5229032
4450 19352.406 178.98756 0 3762.7665 0.10862717
4500 18482.218 340.15496 0 3762.788 12.518301
4550 18359.732 362.83749 0 3762.7879 3.7500902
4600 19623.618 128.71624 0 3762.7196 -1.1328521
4650 17565.707 509.99904 0 3762.9078 1.7135935
4700 19876.052 81.892814 0 3762.6431 0.32476108
4750 19022.676 239.92262 0 3762.6403 -0.24613022
4800 18862.685 269.24248 0 3762.3324 6.2733979
4850 19899.174 77.426145 0 3762.4584 0.42535238
4900 18250.865 382.72867 0 3762.5185 23.308462
4950 18895.847 263.22651 0 3762.4575 8.0634675
5000 19096.705 225.69358 0 3762.1204 3.6816481
5050 16546.294 698.91312 0 3763.0416 17.453618
5100 19501.208 151.20999 0 3762.5449 -1.1231291
5150 19479.879 155.00669 0 3762.3917 -3.983378
5200 17397.818 541.23039 0 3763.0485 6.1109992
5250 18564.869 324.10557 0 3762.0442 9.2244762
5300 16271.663 747.52374 0 3760.7947 -6.5256602
5350 19831.418 89.851887 0 3762.3367 -2.3453958
5400 18723.697 294.67435 0 3762.0256 4.6822081
5450 19547.28 142.21934 0 3762.086 -5.5243408
5500 19415.447 166.68729 0 3762.1404 -9.5658991
5550 18492.721 337.54773 0 3762.1256 6.5184903
5600 19391.389 171.14375 0 3762.1416 -0.53835361
5650 18503.465 334.62751 0 3761.1951 4.6580363
5700 18153.344 399.91064 0 3761.6409 12.851587
5750 18342.297 365.14769 0 3761.8694 2.7148176
5800 19583.241 135.64969 0 3762.1758 -1.089608
5850 15967.283 804.18382 0 3761.088 11.278762
5900 19040.271 235.35509 0 3761.3312 5.1352158
5950 17920.962 443.17951 0 3761.8762 4.9621366
6000 19100.92 224.3946 0 3761.602 -9.537589
6050 17982.119 432.3251 0 3762.3472 -2.851617
6100 16233.096 755.46191 0 3761.5908 25.113316
6150 18316.543 370.01118 0 3761.9635 -1.7445703
6200 18483.464 339.13282 0 3761.9966 -2.0857447
6250 18609.406 315.56032 0 3761.7467 -12.289208
6300 17167.919 582.68212 0 3761.9264 -3.8263397
6350 17870.329 452.58116 0 3761.9013 -3.3843134
6400 19309.717 186.11786 0 3761.9913 -4.9462739
6450 17964.073 435.39924 0 3762.0794 12.272972
6500 18772.847 285.61959 0 3762.0727 6.7928648
6550 18915.116 259.41365 0 3762.213 -4.1449761
6600 19446.628 161.18763 0 3762.415 -2.1906581
6650 16348.787 734.99282 0 3762.546 -9.9624546
6700 19066.684 231.43863 0 3762.3061 -5.362833
6750 14890.323 1004.547 0 3762.0143 37.373013
6800 18235.19 385.253 0 3762.1401 0.21012662
6850 16447.997 716.11276 0 3762.0382 -9.2095411
6900 18343.362 364.81902 0 3761.7379 10.417932
6950 16014.084 797.13348 0 3762.7046 6.7906777
7000 19120.393 221.29236 0 3762.1059 -1.3461375
7050 18055.409 418.30136 0 3761.8957 1.5772317
7100 18407.231 353.41868 0 3762.1652 0.61071769
7150 18728.136 293.64021 0 3761.8136 5.1649654
7200 17706.628 483.07628 0 3762.0815 18.000708
7250 19349.505 178.89673 0 3762.1385 2.540201
7300 20016.293 55.389159 0 3762.1101 -1.5793163
7350 19398.573 169.86661 0 3762.1949 -5.060123
7400 19466.526 157.37407 0 3762.2862 1.7158273
7450 18440.348 347.09196 0 3761.9712 12.781963
7500 19989.907 60.555934 0 3762.3906 -1.5033319
7550 19667.28 120.27403 0 3762.363 -3.3502366
7600 18497.707 336.15863 0 3761.66 1.7887539
7650 17901.957 447.17282 0 3762.3501 0.016725252
7700 19758.725 103.3129 0 3762.3361 -23.534448
7750 19443.957 161.6532 0 3762.386 -10.323924
7800 19776.178 100.1773 0 3762.4324 6.0854422
7850 19242.512 198.86705 0 3762.2952 5.2823659
7900 19499.929 151.30366 0 3762.4017 12.299911
7950 19630.317 127.19541 0 3762.4393 8.0799632
8000 19872.384 82.421129 0 3762.4923 2.2126691
8050 17747.038 476.27982 0 3762.7683 -7.7042786
8100 18832.654 274.78106 0 3762.3095 13.882157
8150 19949.814 68.09711 0 3762.5072 -0.54410896
8200 17555.866 511.02517 0 3762.1115 6.2471175
8250 17800.1 465.9992 0 3762.314 13.583485
8300 19755.224 103.89732 0 3762.2721 -1.487243
8350 17583.61 506.17539 0 3762.3995 -9.7819128
8400 18529.003 330.75623 0 3762.0532 14.731228
8450 20155.902 29.797078 0 3762.3716 -8.5711085
8500 18047.548 420.54645 0 3762.685 7.3875118
8550 19790.794 97.493375 0 3762.4553 -3.3427911
8600 19997.902 59.172074 0 3762.4874 3.3479688
8650 19987.319 61.148363 0 3762.5037 -1.889232
8700 19363.91 176.41833 0 3762.3276 -9.4291288
8750 18712.689 296.3979 0 3761.7107 5.9221369
8800 19783.17 98.860518 0 3762.4105 -3.5262066
8850 18796.049 281.60057 0 3762.3504 -8.2913002
8900 16738.277 662.62261 0 3762.3035 8.5838631
8950 17869.613 452.25006 0 3761.4377 11.561101
9000 18682.512 302.27997 0 3762.0043 3.8878724
9050 17513.759 518.50265 0 3761.7914 23.05778
9100 17500.686 521.57944 0 3762.4473 -2.8435751
9150 19645.683 124.43597 0 3762.5254 -3.0193092
9200 18898.897 262.76552 0 3762.5612 3.5891701
9250 20114.279 37.614866 0 3762.4813 -0.58120871
9300 19562.613 139.54073 0 3762.2468 -3.2630158
9350 19679.811 118.05865 0 3762.468 -3.4644363
9400 19297.384 188.84527 0 3762.4349 0.40498037
9450 18267.029 379.52581 0 3762.309 -0.13762867
9500 19951.072 67.63844 0 3762.2814 -7.575539
9550 19134.562 218.46835 0 3761.9057 -1.9626244
9600 19089.093 227.29178 0 3762.3089 -1.94158
9650 16964.603 620.71289 0 3762.3061 16.987042
9700 18846.881 271.3129 0 3761.4761 3.4458802
9750 19309.225 186.0142 0 3761.7966 9.4048627
9800 16359.704 733.51007 0 3763.0849 15.870164
9850 19958.532 66.203725 0 3762.2282 6.0043645
9900 19864.564 83.502384 0 3762.1253 -0.65360617
9950 18996.789 244.25101 0 3762.1749 -2.4961826
10000 17933.494 441.33587 0 3762.3532 -6.0731708
Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
Performance: 22733.175 tau/day, 2631.155 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
Other | | 0.007383 | | | 0.19
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 612 ave 612 max 612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 612
Ave neighs/atom = 7.55556
Neighbor list builds = 989
Dangerous builds = 906
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

336
examples/rigid/log.5Oct16.rigid.poems2.g++.4
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@ -1,336 +0,0 @@
LAMMPS (5 Oct 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: More than one fix poems (../fix_poems.cpp:352)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 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 = 18 18 18
Memory usage per processor = 3.50303 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47585 0 3765.6103 -17.923459
1500 19223.688 204.15176 0 3764.0939 -1.6134529
1550 18147.996 404.12677 0 3764.8668 8.4194781
1600 18615.043 317.42468 0 3764.6548 -2.3288926
1650 20120.654 38.887908 0 3764.935 -8.7620288
1700 19450.907 162.98267 0 3765.0025 2.3254739
1750 19374.631 177.3797 0 3765.2744 8.9328773
1800 19424.404 167.93965 0 3765.0514 0.081228843
1850 17936.227 442.84645 0 3764.3699 6.6011251
1900 19982.595 64.406244 0 3764.8868 -2.952971
1950 16215.818 761.91942 0 3764.8486 13.994877
2000 18584.433 322.11846 0 3763.6801 7.1653695
2050 20107.965 41.025796 0 3764.723 -0.31089763
2100 20002.329 60.593879 0 3764.7288 -6.7919882
2150 16949.817 626.58598 0 3765.4409 3.5087505
2200 20010.954 58.8082 0 3764.5403 -10.862143
2250 18982.732 247.00854 0 3762.3293 -0.53812607
2300 18401.276 354.88369 0 3762.5274 1.0921058
2350 19390.535 172.93951 0 3763.7793 -3.3524354
2400 16080.475 786.44896 0 3764.3146 -16.201558
2450 18870.293 268.77171 0 3763.2704 11.199749
2500 19688.508 117.54164 0 3763.5617 4.3806994
2550 18870.328 268.87896 0 3763.3841 -5.6641099
2600 17020.211 611.54841 0 3763.4394 6.3081434
2650 18748.838 291.88478 0 3763.8917 2.4175163
2700 19743.991 106.92945 0 3763.224 -0.33916964
2750 19525.446 147.60906 0 3763.4324 -1.6251174
2800 18257.411 381.40184 0 3762.4038 23.39495
2850 18496.796 337.65425 0 3762.9868 4.3657735
2900 20163.418 29.253902 0 3763.2203 1.4431917
2950 16823.317 646.69817 0 3762.1273 4.9041552
3000 19223.007 203.2529 0 3763.069 4.0414458
3050 17391.02 542.93746 0 3763.4968 15.139863
3100 19205.6 206.57791 0 3763.1705 4.8519241
3150 19835.659 90.247763 0 3763.5179 -14.900053
3200 18962.776 251.5838 0 3763.2089 -13.706561
3250 19418.837 167.29058 0 3763.3716 -2.0866468
3300 18628.291 313.69067 0 3763.3742 5.9919715
3350 17465.974 529.14439 0 3763.5841 14.122593
3400 18488.661 339.6186 0 3763.4448 21.526798
3450 19163.152 214.26098 0 3762.9928 4.1888096
3500 18000.27 429.81789 0 3763.2011 5.4734485
3550 19582.423 136.71887 0 3763.0935 -2.5335675
3600 19634.325 127.2219 0 3763.208 -1.9728322
3650 19428.114 165.40707 0 3763.2059 -2.3318779
3700 19861.116 85.356944 0 3763.3414 -3.9097609
3750 19337.239 182.43992 0 3763.4102 -3.3559651
3800 19493.146 153.40349 0 3763.2453 -0.71089657
3850 18607.616 317.74889 0 3763.6037 3.475832
3900 19719.59 111.5553 0 3763.3313 0.58876668
3950 19756.661 104.5522 0 3763.1931 3.7526698
4000 17904.708 447.1673 0 3762.854 12.270654
4050 19588.087 135.80435 0 3763.2279 0.94578945
4100 19065.901 232.38235 0 3763.1048 -2.7495195
4150 18775.075 286.2257 0 3763.0915 -3.7039858
4200 18800.725 281.46601 0 3763.0817 0.15619543
4250 19732.687 108.90618 0 3763.1075 3.0865861
4300 18278.151 377.63653 0 3762.4794 1.5768601
4350 17915.757 445.4804 0 3763.2133 -3.7040484
4400 15987.794 802.41575 0 3763.1183 22.252078
4450 19302.37 188.69495 0 3763.2079 0.91081327
4500 20039.32 52.304099 0 3763.2893 -2.0828905
4550 19535.953 145.4374 0 3763.2064 -3.3804255
4600 19700.723 114.79823 0 3763.0803 -1.1761163
4650 17804.641 465.85788 0 3763.0136 7.5947192
4700 19913.881 75.240289 0 3762.996 -2.1100557
4750 19982.484 62.535995 0 3762.996 -4.5821237
4800 17400.76 540.21707 0 3762.58 -5.8418778
4850 19199.88 206.90989 0 3762.4433 3.4536341
4900 19173.92 212.11327 0 3762.8392 5.0387071
4950 19236.635 200.57537 0 3762.9152 -1.4932783
5000 19077.616 230.04967 0 3762.9415 4.3742655
5050 19893.763 78.909747 0 3762.94 -1.5796711
5100 18884.746 265.68301 0 3762.8583 2.2767949
5150 17417.096 537.54036 0 3762.9286 -2.8632555
5200 18247.844 383.60092 0 3762.8312 10.384179
5250 19494.107 152.60532 0 3762.6251 -4.7617287
5300 18739.781 292.46206 0 3762.7919 23.210048
5350 19310.938 186.62363 0 3762.7232 14.895327
5400 19540.39 144.14287 0 3762.7336 6.094624
5450 20074.459 45.247888 0 3762.7403 -2.0871835
5500 19986.377 61.668045 0 3762.849 -2.4551918
5550 19038.904 237.07578 0 3762.7987 5.4250813
5600 19439.124 163.1438 0 3762.9816 4.1291468
5650 19480.321 155.58325 0 3763.0501 -3.5308058
5700 19869.291 83.651379 0 3763.1497 -7.8661592
5750 19991.447 61.068554 0 3763.1884 -6.8473586
5800 19454.072 160.36805 0 3762.9739 1.527662
5850 17994.409 430.95597 0 3763.2539 -5.6078082
5900 19209.794 205.74997 0 3763.1193 8.4113055
5950 19046.427 236.06321 0 3763.1793 10.463356
6000 19409.899 168.95271 0 3763.3785 2.542067
6050 18068.174 417.35443 0 3763.3125 10.498199
6100 19549.253 143.21885 0 3763.4509 2.3075797
6150 18464.719 344.0303 0 3763.4228 0.46469762
6200 19811.205 94.62725 0 3763.3689 1.2382763
6250 18715.36 297.26445 0 3763.0718 -3.4541762
6300 17115.664 594.09913 0 3763.6666 4.2065564
6350 18155.927 400.71764 0 3762.9264 1.1521258
6400 19873.093 83.169067 0 3763.3716 0.16383592
6450 19991.88 61.13218 0 3763.3321 -1.3008128
6500 19434.416 164.40698 0 3763.3728 -13.593422
6550 19855.253 86.645329 0 3763.544 -0.85704037
6600 19251.141 198.41152 0 3763.4376 4.3027745
6650 19741.815 107.69047 0 3763.582 4.994835
6700 19633.466 127.69333 0 3763.5203 6.3677145
6750 16231.353 757.83705 0 3763.6431 -1.5978692
6800 18863.396 270.1114 0 3763.3329 -11.915909
6850 19644.779 125.29421 0 3763.2163 -1.151217
6900 18883.642 266.06889 0 3763.0397 -4.3950749
6950 19042.364 236.54144 0 3762.9052 5.5718878
7000 18351.868 364.38028 0 3762.8743 7.8958273
7050 19981.031 62.840667 0 3763.0316 -5.8572298
7100 19796.372 97.073665 0 3763.0685 -3.5178361
7150 19805.385 95.235221 0 3762.899 -2.5481726
7200 18722.055 295.86113 0 3762.9084 13.826356
7250 19537.304 144.54234 0 3762.5616 1.2288666
7300 18787.328 283.49504 0 3762.6299 9.0044469
7350 18886.005 265.52121 0 3762.9295 6.6791881
7400 19891.864 79.239278 0 3762.9178 -2.3882842
7450 18164.752 399.07065 0 3762.9137 3.9400481
7500 18702.612 299.582 0 3763.0286 4.7987316
7550 19884.986 80.231665 0 3762.6365 -0.75016515
7600 19549.059 142.16243 0 3762.3586 -2.1035756
7650 18223.668 387.9047 0 3762.658 -17.064339
7700 19428.4 164.79531 0 3762.6473 -2.8342541
7750 19239.584 199.93029 0 3762.8163 3.1746033
7800 19458.005 159.46176 0 3762.7961 1.714515
7850 18320.308 369.77051 0 3762.4202 2.1422976
7900 18817.415 278.04812 0 3762.7546 0.94492621
7950 19892.761 79.115928 0 3762.9606 1.4948501
8000 19592.344 134.7639 0 3762.9758 -1.8520224
8050 19316.109 185.70579 0 3762.7631 -4.8061205
8100 19867.017 83.850395 0 3762.9277 -3.496391
8150 19129.936 220.29802 0 3762.8789 -2.8357376
8200 18449.554 346.30415 0 3762.8883 1.4417837
8250 18405.197 354.49049 0 3762.8602 6.7020283
8300 18310.437 372.25376 0 3763.0755 3.9043508
8350 18842.702 273.55075 0 3762.94 -10.987272
8400 18574.308 323.33378 0 3763.0204 12.008785
8450 15368.628 918.21692 0 3764.2591 34.80292
8500 18432.887 349.54013 0 3763.0378 0.00064258465
8550 15777.73 841.79263 0 3763.5945 15.473699
8600 17205.381 576.4515 0 3762.6331 2.3985544
8650 19773.742 101.48276 0 3763.2869 2.3978892
8700 19059.824 232.99716 0 3762.5941 5.2611349
8750 19006.086 243.41125 0 3763.0568 4.7880403
8800 19492.691 153.0188 0 3762.7763 1.9118755
8850 19625.883 128.44474 0 3762.8675 3.4157389
8900 19916.97 74.635094 0 3762.9629 -10.157254
8950 16012.956 798.16801 0 3763.5302 16.904998
9000 19364.051 177.00354 0 3762.9389 -13.373346
9050 19133.929 219.61882 0 3762.9389 -7.3824392
9100 18657.168 307.85939 0 3762.8905 9.3071421
9150 17975.904 434.21548 0 3763.0867 6.9609506
9200 19075.282 230.41699 0 3762.8767 7.0961232
9250 20115.276 37.578674 0 3762.6298 1.8678552
9300 18195.486 393.20682 0 3762.7413 13.272552
9350 19617.155 129.85893 0 3762.6653 -2.0849447
9400 19276.325 193.03425 0 3762.724 -2.8963555
9450 18642.803 310.4759 0 3762.8467 3.407984
9500 19175.951 211.72785 0 3762.8298 -0.39025564
9550 17669.191 490.85942 0 3762.9319 5.3867954
9600 18481.199 340.29485 0 3762.7391 8.9004886
9650 20091.442 42.504743 0 3763.1422 -1.3206133
9700 19651.405 124.04835 0 3763.1975 1.4000525
9750 19138.245 219.03637 0 3763.1558 5.8352794
9800 19189.146 209.67958 0 3763.2251 6.214691
9850 19899.376 78.096337 0 3763.166 -0.75102404
9900 19447.247 161.27279 0 3762.6149 -6.4166376
9950 19807.083 95.152663 0 3763.1309 -0.88933698
10000 18972.157 249.56342 0 3762.9258 1.9189241
Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms
Performance: 21628.565 tau/day, 2503.306 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74
Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53
Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46
Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12
Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58
Other | | 0.02291 | | | 0.57
Nlocal: 20.25 ave 37 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 17.75 ave 33 max 4 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 144.75 ave 356 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 579
Ave neighs/atom = 7.14815
Neighbor list builds = 994
Dangerous builds = 958
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

452
examples/rigid/log.5Oct16.rigid.tnr.g++.1
View File

@ -1,452 +0,0 @@
LAMMPS (5 Oct 2016)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 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 = 45 45 45
Memory usage per processor = 7.32042 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms
Performance: 331401.531 tau/day, 767.133 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
Other | | 0.1774 | | | 2.72
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5254 ave 5254 max 5254 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5254
Ave neighs/atom = 0.938214
Ave special neighs/atom = 0.571429
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Memory usage per processor = 7.32042 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms
Performance: 315008.398 tau/day, 729.186 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
Other | | 0.03562 | | | 2.60
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1347 ave 1347 max 1347 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5399 ave 5399 max 5399 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5399
Ave neighs/atom = 0.964107
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Memory usage per processor = 7.32042 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
Performance: 311550.061 tau/day, 721.181 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
Other | | 0.03559 | | | 2.57
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1284 ave 1284 max 1284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5677 ave 5677 max 5677 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5677
Ave neighs/atom = 1.01375
Ave special neighs/atom = 0.571429
Neighbor list builds = 151
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Memory usage per processor = 7.32042 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
Performance: 141281.224 tau/day, 327.040 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
Other | | 0.04962 | | | 1.62
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2963 ave 2963 max 2963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25797 ave 25797 max 25797 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25797
Ave neighs/atom = 4.60661
Ave special neighs/atom = 0.571429
Neighbor list builds = 334
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Memory usage per processor = 7.32428 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
Performance: 146727.069 tau/day, 339.646 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
Other | | 0.03878 | | | 1.32
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3244 ave 3244 max 3244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 30929 ave 30929 max 30929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30929
Ave neighs/atom = 5.52304
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Memory usage per processor = 7.32428 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
Performance: 137864.384 tau/day, 319.131 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
Other | | 0.03924 | | | 1.25
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3635 ave 3635 max 3635 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38235 ave 38235 max 38235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38235
Ave neighs/atom = 6.82768
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Memory usage per processor = 7.32811 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
Performance: 134004.591 tau/day, 310.196 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
Other | | 0.03903 | | | 1.21
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3799 ave 3799 max 3799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39646 ave 39646 max 39646 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39646
Ave neighs/atom = 7.07964
Ave special neighs/atom = 0.571429
Neighbor list builds = 158
Dangerous builds = 0
Total wall time: 0:00:21

452
examples/rigid/log.5Oct16.rigid.tnr.g++.4
View File

@ -1,452 +0,0 @@
LAMMPS (5 Oct 2016)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 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 = 45 45 45
Memory usage per processor = 6.96454 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms
Performance: 686709.553 tau/day, 1589.605 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05
Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82
Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94
Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51
Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09
Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32
Other | | 0.1658 | | | 5.27
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 648.25 ave 688 max 598 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1202.5 ave 1821 max 698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 4810
Ave neighs/atom = 0.858929
Ave special neighs/atom = 0.571429
Neighbor list builds = 759
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms
Performance: 579437.739 tau/day, 1341.291 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48
Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54
Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13
Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51
Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07
Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08
Other | | 0.03125 | | | 4.19
Nlocal: 1400 ave 1868 max 935 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 633.75 ave 695 max 541 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1263 ave 1799 max 710 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5052
Ave neighs/atom = 0.902143
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms
Performance: 567665.504 tau/day, 1314.041 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58
Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52
Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41
Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25
Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07
Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58
Other | | 0.02726 | | | 3.58
Nlocal: 1400 ave 1832 max 970 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 652.5 ave 749 max 561 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1407.5 ave 2071 max 748 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 5630
Ave neighs/atom = 1.00536
Ave special neighs/atom = 0.571429
Neighbor list builds = 149
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms
Performance: 307209.818 tau/day, 711.134 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72
Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23
Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07
Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56
Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03
Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12
Other | | 0.04594 | | | 3.27
Nlocal: 1400 ave 1820 max 1010 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 1576 ave 1694 max 1470 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 6543 ave 9989 max 3497 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 26172
Ave neighs/atom = 4.67357
Ave special neighs/atom = 0.571429
Neighbor list builds = 337
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms
Performance: 308990.110 tau/day, 715.255 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77
Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27
Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80
Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50
Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03
Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58
Other | | 0.04265 | | | 3.05
Nlocal: 1400 ave 1770 max 1095 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1578.5 ave 1693 max 1493 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 7868 ave 12041 max 4579 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 31472
Ave neighs/atom = 5.62
Ave special neighs/atom = 0.571429
Neighbor list builds = 167
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms
Performance: 312625.215 tau/day, 723.669 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51
Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28
Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29
Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07
Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03
Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25
Other | | 0.03557 | | | 2.57
Nlocal: 1400 ave 1669 max 1139 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1761.5 ave 1898 max 1632 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 9311.75 ave 12525 max 5959 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 37247
Ave neighs/atom = 6.65125
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms
Performance: 316143.197 tau/day, 731.813 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17
Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31
Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56
Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48
Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03
Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05
Other | | 0.03282 | | | 2.40
Nlocal: 1400 ave 1607 max 1199 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1819.25 ave 1940 max 1712 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 9882 ave 12628 max 7201 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 39528
Ave neighs/atom = 7.05857
Ave special neighs/atom = 0.571429
Neighbor list builds = 156
Dangerous builds = 0
Total wall time: 0:00:10

127
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.160
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.16
Lattice spacing in x,y,z = 3.16 3.16 3.16
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000223637 secs
mass 1 183.84
# choose potential
include Mo_Chen_PRM2017.snap
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
SNAP Element = Mo, Radius 0.5, Weight 1
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
SNAP keyword rcutfac 4.615858
SNAP keyword twojmax 6
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.61586
ghost atom cutoff = 5.61586
binsize = 2.80793, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -22.405975 0 -22.3675 2575.7657
10 294.77555 -22.405305 0 -22.3675 2756.6894
20 279.53011 -22.40335 0 -22.3675 3285.8272
30 255.52174 -22.40027 0 -22.3675 4122.8933
40 224.7299 -22.396321 0 -22.367499 5204.3499
50 189.67529 -22.391825 0 -22.367499 6449.1308
60 153.18862 -22.387145 0 -22.367499 7765.911
70 118.14998 -22.382652 0 -22.367499 9061.1616
80 87.224916 -22.378685 0 -22.367499 10247.68
90 62.623892 -22.37553 0 -22.367498 11250.067
100 45.9103 -22.373386 0 -22.367498 12011.726
Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms
Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01
Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01
Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01
Other | | 0.0002868 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7424 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

127
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.160
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.16
Lattice spacing in x,y,z = 3.16 3.16 3.16
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000277281 secs
mass 1 183.84
# choose potential
include Mo_Chen_PRM2017.snap
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
SNAP Element = Mo, Radius 0.5, Weight 1
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
SNAP keyword rcutfac 4.615858
SNAP keyword twojmax 6
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.61586
ghost atom cutoff = 5.61586
binsize = 2.80793, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -22.405975 0 -22.3675 2575.7657
10 294.63153 -22.405286 0 -22.3675 2753.4662
20 278.98535 -22.40328 0 -22.3675 3272.416
30 254.38916 -22.400125 0 -22.3675 4091.8933
40 222.91191 -22.396088 0 -22.367499 5148.5505
50 187.16984 -22.391504 0 -22.367499 6362.2454
60 150.08253 -22.386747 0 -22.367499 7643.2732
70 114.60307 -22.382197 0 -22.367499 8900.2448
80 83.449257 -22.378201 0 -22.367499 10047.619
90 58.862643 -22.375048 0 -22.367498 11012.233
100 42.41931 -22.372939 0 -22.367498 11740.641
Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms
Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63
Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03
Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01
Other | | 0.00481 | | | 0.25
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1856 ave 1856 max 1856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

51
examples/snap/log.5Oct16.snap.Ta06A.g++.1 → examples/snap/log.20Apr18.snap.Ta06A.g++.1
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@ -1,4 +1,6 @@
LAMMPS (5 Oct 2016)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000328064 secs
mass 1 180.88
# choose potential
include Ta06A_pot.snap
include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 4.8
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
# Setup output
@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.8
ghost atom cutoff = 5.8
binsize = 2.9 -> bins = 5 5 5
Memory usage per processor = 2.92823 Mbytes
binsize = 2.9, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.96579 -11.851053 0 -11.813095 2696.1559
@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 124.04276 -11.829003 0 -11.813094 1537.703
90 97.37622 -11.825582 0 -11.813094 1734.9662
100 75.007873 -11.822714 0 -11.813094 1930.8005
Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms
Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms
Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97
Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01
Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00
Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01
Other | | 0.0002978 | | | 0.01
Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02
Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01
Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01
Other | | 0.0003583 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:02

51
examples/snap/log.5Oct16.snap.Ta06A.g++.4 → examples/snap/log.20Apr18.snap.Ta06A.g++.4
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@ -1,4 +1,6 @@
LAMMPS (5 Oct 2016)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000288486 secs
mass 1 180.88
# choose potential
include Ta06A_pot.snap
include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
pair_style hybrid/overlay snap zbl 4 4.8
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
# Setup output
@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.8
ghost atom cutoff = 5.8
binsize = 2.9 -> bins = 5 5 5
Memory usage per processor = 2.91109 Mbytes
binsize = 2.9, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.8664 -11.85104 0 -11.813095 2702.935
@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 121.80051 -11.828715 0 -11.813094 1627.6911
90 95.262635 -11.825311 0 -11.813094 1812.9327
100 73.194645 -11.822481 0 -11.813094 1995.2199
Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms
Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms
Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 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 | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29
Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58
Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03
Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01
Other | | 0.0008071 | | | 0.09
Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72
Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04
Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01
Other | | 0.001728 | | | 0.13
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
Total wall time: 0:00:01

34
examples/snap/log.21Feb17.snap.W.2940.g++.1 → examples/snap/log.20Apr18.snap.W.2940.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (13 Feb 2017)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000190258 secs
mass 1 183.84
# choose potential
include W_2940_2017_2.pot.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
include W_2940_2017_2.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 5.14696 Mbytes
Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.40666 -11.027479 0 -10.989849 3246.0559
@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 58.605244 -10.997364 0 -10.989848 11289.914
90 39.754503 -10.994946 0 -10.989848 11824.945
100 32.524085 -10.994019 0 -10.989848 11932.118
Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms
Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms
Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 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 | 11.826 | 11.826 | 11.826 | 0.0 | 99.99
Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00
Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00
Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00
Other | | 0.0002718 | | | 0.00
Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00
Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00
Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00
Other | | 0.0003347 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11
Total wall time: 0:00:09

34
examples/snap/log.21Feb17.snap.W.2940.g++.4 → examples/snap/log.20Apr18.snap.W.2940.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (13 Feb 2017)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000309944 secs
mass 1 183.84
# choose potential
include W_2940_2017_2.pot.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
include W_2940_2017_2.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 5.12833 Mbytes
Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.22504 -11.027456 0 -10.989849 3258.275
@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 56.127265 -10.997046 0 -10.989848 11551.687
90 38.025013 -10.994724 0 -10.989847 12069.936
100 31.768127 -10.993922 0 -10.989847 12145.648
Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms
Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms
Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 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 | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39
Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58
Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01
Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00
Other | | 0.000698 | | | 0.02
Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49
Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02
Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00
Other | | 0.002315 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:05

40
examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 → examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (13 Feb 2017)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000431538 secs
mass 1 183.84
mass 2 4.0026
@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
include W.SNAP_HePair.pot
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
include W_2940_2017_2_He_JW2013.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 7.6729 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 290.48923 -10.436885 0 -10.399629 -5646.4813
@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 85.903126 -10.410645 0 -10.399628 857.74986
90 65.223651 -10.407993 0 -10.399628 1494.2746
100 59.833542 -10.407302 0 -10.399628 1938.9164
Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
Loop time of 8.902 on 1 procs for 100 steps with 128 atoms
Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 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 | 11.072 | 11.072 | 11.072 | 0.0 | 99.99
Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00
Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00
Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00
Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00
Other | | 0.0003119 | | | 0.00
Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98
Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00
Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01
Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00
Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00
Other | | 0.0003953 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:11
Total wall time: 0:00:09

38
examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 → examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (13 Feb 2017)
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
Time spent = 0.000274658 secs
mass 1 183.84
mass 2 4.0026
@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
include W.SNAP_HePair.pot
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
include W_2940_2017_2_He_JW2013.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 7.65426 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 292.13979 -10.437097 0 -10.39963 -5516.3963
@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 79.985938 -10.409886 0 -10.399628 2392.1106
90 62.568933 -10.407652 0 -10.399628 3141.7027
100 56.697933 -10.406899 0 -10.399628 3583.9538
Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms
Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms
Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 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 | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79
Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17
Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01
Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00
Other | | 0.0006654 | | | 0.02
Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00
Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02
Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00
Other | | 0.002119 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:04

12
lib/atc/ATC_Method.cpp
View File

@ -2015,8 +2015,8 @@ pecified
LammpsInterface::instance()->int_allmax(&send_size,&max_size);
if (comm_rank == 0) {
int intbuf[max_size];
double buf[max_size];
int *intbuf = new int[max_size];
double *buf = new double[max_size];
for (int iproc = 1; iproc < nprocs; iproc++) {
LammpsInterface::instance()->int_recv(intbuf,max_size,iproc);
LammpsInterface::instance()->recv(buf,max_size,iproc);
@ -2024,15 +2024,19 @@ pecified
out << intbuf[i] << " " << buf[i] << "\n";
}
}
delete[] intbuf;
delete[] buf;
} else {
int intbuf[send_size];
double buf[send_size];
int *intbuf = new int[send_size];
double *buf = new double[send_size];
for (int i = 0; i < send_size; i++) {
intbuf[i] = id2tag[i];
buf[i] = atomicVolumeMatrix(i,i);
}
LammpsInterface::instance()->int_send(intbuf,send_size);
LammpsInterface::instance()->send(buf,send_size);
delete[] intbuf;
delete[] buf;
}
}

2
lib/atc/Array.h
View File

@ -4,7 +4,7 @@
#include <cstdlib>
#include <iostream>
#include <string>
#include <stdio.h>
#include <cstdio>
// for macros
#include "MatrixDef.h"

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