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lammps
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Merge branch 'master' into kim-v2-update

This commit is contained in:
Ryan S. Elliott 2018-10-01 21:17:26 -05:00
parent 634ed487a5 4fe23c3854
commit f61f43a56b
800 changed files with 47457 additions and 2680 deletions
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68
.github/CODEOWNERS vendored
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@ -17,6 +17,7 @@ src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
@ -29,19 +30,86 @@ src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-SCAFACOS/* @rhalver
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/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-MISC/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
# core LAMMPS classes
src/lammps.* @sjplimp
src/pointers.h @sjplimp
src/atom.* @sjplimp
src/atom_vec.* @sjplimp
src/angle.* @sjplimp
src/bond.* @sjplimp
src/comm*.* @sjplimp
src/compute.* @sjplimp
src/dihedral.* @sjplimp
src/domain.* @sjplimp
src/dump*.* @sjplimp
src/error.* @sjplimp
src/finish.* @sjplimp
src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/main.cpp @sjplimp
src/memory.* @sjplimp
src/modify.* @sjplimp
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
src/npair*.* @sjplimp
src/ntopo*.* @sjplimp
src/nstencil*.* @sjplimp
src/neighbor.* @sjplimp
src/nbin*.* @sjplimp
src/neigh_*.* @sjplimp
src/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp
src/random_*.* @sjplimp
src/region*.* @sjplimp
src/rcb.* @sjplimp
src/read*.* @sjplimp
src/rerun.* @sjplimp
src/run.* @sjplimp
src/respa.* @sjplimp
src/set.* @sjplimp
src/special.* @sjplimp
src/suffix.h @sjplimp
src/thermo.* @sjplimp
src/universe.* @sjplimp
src/update.* @sjplimp
src/variable.* @sjplimp
src/verlet.* @sjplimp
src/velocity.* @sjplimp
src/write_data.* @sjplimp
src/write_restart.* @sjplimp
# overrides for specific files
src/dump_movie.* @akohlmey
src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
# tools
tools/msi2lmp/* @akohlmey

2
.gitignore vendored
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@ -1,6 +1,7 @@
*~
*.o
*.so
*.lo
*.cu_o
*.ptx
*_ptx.h
@ -32,6 +33,7 @@ log.cite
.Trashes
ehthumbs.db
Thumbs.db
.clang-format
#cmake
/build*

286
cmake/CMakeLists.txt
View File

@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT
# To avoid conflicts with the conventional Makefile build system, we build everything here
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
@ -43,6 +43,29 @@ function(validate_option name values)
endif()
endfunction(validate_option)
function(get_lammps_version version_header variable)
file(READ ${version_header} line)
set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
string(STRIP ${day} day)
string(STRIP ${month} month)
string(STRIP ${year} year)
list(FIND MONTHS "${month}" month)
string(LENGTH ${day} day_length)
string(LENGTH ${month} month_length)
if(day_length EQUAL 1)
set(day "0${day}")
endif()
if(month_length EQUAL 1)
set(month "0${month}")
endif()
set(${variable} "${year}${month}${day}" PARENT_SCOPE)
endfunction()
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
@ -113,6 +136,7 @@ if(BUILD_EXE)
if(LAMMPS_MACHINE)
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
endif()
set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
endif()
option(BUILD_LIB "Build LAMMPS library" OFF)
@ -121,10 +145,10 @@ if(BUILD_LIB)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
mark_as_advanced(LIB_SUFFIX)
if(LIB_SUFFIX)
set(LIB_SUFFIX "_${LIB_SUFFIX}")
set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
mark_as_advanced(LAMMPS_LIB_SUFFIX)
if(LAMMPS_LIB_SUFFIX)
set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
endif()
endif()
@ -139,6 +163,35 @@ set(LAMMPS_LINK_LIBS)
set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE 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-PTM USER-QTB USER-REAXC USER-SCAFACOS 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)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
enable_language(Fortran)
endif()
if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
enable_language(C)
endif()
# do MPI detection after language activation, if MPI for these language is required
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI)
@ -183,25 +236,52 @@ endif()
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING)
if(ENABLE_TESTING AND BUILD_EXE)
enable_testing()
endif(ENABLE_TESTING)
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE 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)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
include(FetchContent)
FetchContent_Declare(lammps-testing
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
)
FetchContent_GetProperties(lammps-testing)
if(NOT lammps-testing_POPULATED)
message(STATUS "Downloading tests...")
FetchContent_Populate(lammps-testing)
endif()
set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
endif()
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
foreach(script_path ${TEST_SCRIPTS})
get_filename_component(TEST_NAME ${script_path} EXT)
get_filename_component(SCRIPT_NAME ${script_path} NAME)
get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
set(TEST_NAME "test_core_${TEST_NAME}_serial")
add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
list(LENGTH TEST_SCRIPTS NUM_TESTS)
message(STATUS "Found ${NUM_TESTS} tests.")
endif()
endif()
macro(pkg_depends PKG1 PKG2)
if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
@ -215,17 +295,7 @@ pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
######################################################
# packages with special compiler needs or external libs
######################################################
if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
enable_language(Fortran)
endif()
if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
enable_language(C)
endif()
pkg_depends(USER-SCAFACOS MPI)
find_package(OpenMP QUIET)
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
@ -279,7 +349,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
else()
@ -403,6 +473,57 @@ if(PKG_LATTE)
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
if(PKG_USER-SCAFACOS)
find_package(GSL REQUIRED)
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
if(DOWNLOAD_SCAFACOS)
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
--disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw
--with-internal-pfft
--with-internal-pnfft
$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
F77=
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
list(APPEND LAMMPS_DEPS scafacos_build)
# list and order from pkg_config file of ScaFaCoS build
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
else()
FIND_PACKAGE(PkgConfig REQUIRED)
PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
endif()
include_directories(${SCAFACOS_INCLUDE_DIRS})
endif()
if(PKG_USER-MOLFILE)
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@ -412,8 +533,8 @@ endif()
if(PKG_USER-NETCDF)
find_package(NetCDF REQUIRED)
include_directories(NETCDF_INCLUDE_DIR)
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
include_directories(${NETCDF_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
@ -430,8 +551,9 @@ if(PKG_USER-SMD)
set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3)
if(NOT Eigen3_FOUND)
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
@ -481,6 +603,40 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
if(PKG_MESSAGE)
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
if(BUILD_SHARED_LIBS)
add_library(cslib SHARED ${cslib_SOURCES})
else()
add_library(cslib STATIC ${cslib_SOURCES})
endif()
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
if(MESSAGE_ZMQ)
target_compile_definitions(cslib PRIVATE -DZMQ_YES)
find_package(ZMQ REQUIRED)
target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
else()
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
endif()
list(APPEND LAMMPS_LINK_LIBS cslib)
include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
endif()
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
@ -567,8 +723,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
foreach(PKG ${DEFAULT_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -586,8 +742,8 @@ endforeach()
foreach(PKG ${ACCEL_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -601,8 +757,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
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
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
@ -677,13 +835,16 @@ 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
${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
@ -883,7 +1044,7 @@ if(PKG_GPU)
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
@ -896,15 +1057,15 @@ if(PKG_GPU)
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
@ -953,7 +1114,7 @@ if(PKG_GPU)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
foreach(GPU_KERNEL ${GPU_LIB_CU})
@ -1011,7 +1172,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
######################################
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n")
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
list(SORT temp_PKG_LIST)
foreach(PKG ${temp_PKG_LIST})
if(PKG_${PKG})
set(temp "${temp} \"${PKG}\",\n")
endif()
@ -1036,14 +1199,14 @@ if(BUILD_LIB)
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
if(BUILD_SHARED_LIBS)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
endif()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
@ -1059,10 +1222,11 @@ if(BUILD_EXE)
endif()
endif()
set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(ENABLE_TESTING)
add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
add_test(ShowHelp ${LAMMPS_BINARY} -help)
endif()
endif()
@ -1077,7 +1241,7 @@ if(BUILD_DOC)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
@ -1130,7 +1294,7 @@ endif()
# Install potential files in data directory
###############################################################################
set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
@ -1172,7 +1336,7 @@ endif()
###############################################################################
# Print package summary
###############################################################################
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()

48
cmake/FindLAMMPS.cmake.in Normal file
View File

@ -0,0 +1,48 @@
# - Find liblammps
# Find the native liblammps headers and libraries.
#
# The following variables will set:
# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
# LAMMPS_LIBRARIES - List of libraries when using lammps.
# LAMMPS_API_DEFINES - lammps library api defines
# LAMMPS_VERSION - lammps library version
# LAMMPS_FOUND - True if liblammps found.
#
# In addition a LAMMPS::LAMMPS imported target is getting created.
#
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
#
# See the README file in the top-level LAMMPS directory.
#
find_package(PkgConfig)
pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
set(LAMMPS_VERSION @LAMMPS_VERSION@)
set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
endif()

8
cmake/Modules/FindZMQ.cmake Normal file
View File

@ -0,0 +1,8 @@
find_path(ZMQ_INCLUDE_DIR zmq.h)
find_library(ZMQ_LIBRARY NAMES zmq)
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)

15
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -48,8 +48,13 @@ function(CreateStyleHeader path filename)
set(temp "")
if(ARGC GREATER 2)
list(REMOVE_AT ARGV 0 1)
set(header_list)
foreach(FNAME ${ARGV})
get_filename_component(FNAME ${FNAME} NAME)
list(APPEND header_list ${FNAME})
endforeach()
list(SORT header_list)
foreach(FNAME ${header_list})
set(temp "${temp}#include \"${FNAME}\"\n")
endforeach()
endif()
@ -80,19 +85,23 @@ function(RegisterNPairStyle path)
AddStyleHeader(${path} NPAIR)
endfunction(RegisterNPairStyle)
function(RegisterFixStyle path)
AddStyleHeader(${path} FIX)
endfunction(RegisterFixStyle)
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor

6
cmake/pkgconfig/liblammps.pc.in
View File

@ -4,15 +4,15 @@
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
prefix=@CMAKE_INSTALL_FULL_PREFIX@
prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
Version:
Version: @LAMMPS_VERSION@
Requires:
Libs: -L${libdir} -llammps@LIB_SUFFIX@@
Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@

45
doc/lammps.1 Normal file
View File

@ -0,0 +1,45 @@
.TH LAMMPS "2018-08-22"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
.SH SYNOPSIS
.B lmp
-in in.file
or
mpirun \-np 2
.B lmp
-in in.file
.SH DESCRIPTION
.B LAMMPS
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
materials (biomolecules, polymers) and solid-state materials (metals,
semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale.
See http://lammps.sandia.gov/ for documentation.
.SH OPTIONS
See https://lammps.sandia.gov/doc/Run_options.html for details on
command-line options.
.SH COPYRIGHT
© 2003--2018 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-2'.

4
doc/src/Build_basics.txt
View File

@ -292,6 +292,10 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
NOTE: You can also download a tarball of the documention for the
current LAMMPS version (HTML and PDF files), from the website
"download page"_http://lammps.sandia.gov/download.html.
:line
Install LAMMPS after a build :h4,link(install)

74
doc/src/Build_extras.txt
View File

@ -31,6 +31,7 @@ This is the list of packages that may require additional steps.
"KOKKOS"_#kokkos,
"LATTE"_#latte,
"MEAM"_#meam,
"MESSAGE"_#message,
"MSCG"_#mscg,
"OPT"_#opt,
"POEMS"_#poems,
@ -47,6 +48,7 @@ This is the list of packages that may require additional steps.
"USER-OMP"_#user-omp,
"USER-QMMM"_#user-qmmm,
"USER-QUIP"_#user-quip,
"USER-SCAFACOS"_#user-scafacos,
"USER-SMD"_#user-smd,
"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
@ -361,6 +363,10 @@ make lib-meam args="-m mpi" # build with default Fortran compiler compatible
make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
the other on your system.
The build should produce two files: lib/meam/libmeam.a and
lib/meam/Makefile.lammps. The latter is copied from an existing
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
@ -373,6 +379,35 @@ file.
:line
MESSAGE package :h4,link(message)
This package can optionally include support for messaging via sockets,
using the open-source "ZeroMQ library"_http://zeromq.org, which must
be installed on your system.
[CMake build]:
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
[Traditional make]:
Before building LAMMPS, you must build the CSlib library in
lib/message. You can build the CSlib library manually if you prefer;
follow the instructions in lib/message/README. You can also do it in
one step from the lammps/src dir, using a command like these, which
simply invoke the lib/message/Install.py script with the specified args:
make lib-message # print help message
make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
make lib-message args="-s" # build as serial lib with no ZMQ support
The build should produce two files: lib/message/cslib/src/libmessage.a
and lib/message/Makefile.lammps. The latter is copied from an
existing Makefile.lammps.* and has settings to link with the ZeroMQ
library if requested in the build.
:line
MSCG package :h4,link(mscg)
To build with this package, you must download and build the MS-CG
@ -894,6 +929,45 @@ successfully build on your system.
:line
USER-SCAFACOS package :h4,link(user-scafacos)
To build with this package, you must download and build the "ScaFaCoS
Coulomb solver library"_scafacos_home
:link(scafacos_home,http://www.scafacos.de)
[CMake build]:
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre
If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
and built inside the CMake build directory. If the ScaFaCoS library
is already on your system (in a location CMake cannot find it),
SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR
is the directory the ScaFaCoS include file is in.
[Traditional make]:
You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in lib/scafacos/README. You can also
do it in one step from the lammps/src dir, using a command like these,
which simply invoke the lib/scafacos/Install.py script with the
specified args:
make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
Note that 2 symbolic (soft) links, "includelink" and "liblink", are
created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the lib/scafacos/Makefile.lammps file.
:line
USER-SMD package :h4,link(user-smd)
To build with this package, you must download the Eigen3 library.

2
doc/src/Build_package.txt
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@ -42,6 +42,7 @@ packages:
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MEAM"_Build_extras.html#meam,
"MESSAGE"_Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
@ -58,6 +59,7 @@ packages:
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
"USER-SCAFACOS"_Build_extras.html#user-scafacos,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)

2
doc/src/Commands_all.txt
View File

@ -71,6 +71,7 @@ An alphabetic list of all LAMMPS commands.
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
@ -103,6 +104,7 @@ An alphabetic list of all LAMMPS commands.
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,

3
doc/src/Commands_compute.txt
View File

@ -35,6 +35,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"chunk/spread/atom"_compute_chunk_spread_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"cnp/atom"_compute_cnp_atom.html,
@ -95,8 +96,10 @@ KOKKOS, o = USER-OMP, t = OPT.
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
"ptm/atom"_compute_ptm_atom.html
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.html,
"reduce/region"_compute_reduce.html,
"rigid/local"_compute_rigid_local.html,
"saed"_compute_saed.html,

3
doc/src/Commands_kspace.txt
View File

@ -33,4 +33,5 @@ OPT.
"pppm/disp (i)"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/stagger"_kspace_style.html,
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
"pppm/tip4p (o)"_kspace_style.html,
"scafacos"_kspace_style.html :tb(c=4,ea=c)

1
doc/src/Commands_pair.txt
View File

@ -33,6 +33,7 @@ OPT.
"agni (o)"_pair_agni.html,
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
"atm"_pair_atm.html,
"awpmd/cut"_pair_awpmd.html,
"beck (go)"_pair_beck.html,
"body/nparticle"_pair_body_nparticle.html,

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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
\begin{equation}
E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
\end{equation}
\end{document}

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doc/src/Eqs/ptm_rmsd.tex Normal file
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@ -0,0 +1,21 @@
\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
\begin{document}
\begin{equation*}
\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
\norm{
s[\vec{u_i} - \mean{\set{u}}]
-
\set{Q} \vec{v_i}
}^2}
\end{equation*}
\end{document}

4
doc/src/Howto.txt
View File

@ -54,6 +54,7 @@ General howto :h3
Howto_replica
Howto_library
Howto_couple
Howto_client_server
END_RST -->
@ -64,7 +65,8 @@ END_RST -->
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
"Couple LAMMPS to other codes"_Howto_couple.html
"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
<!-- END_HTML_ONLY -->

45
doc/src/Howto_chunk.txt
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@ -22,7 +22,7 @@ commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 3 kinds of chunk-related commands is briefly
Here, each of the 4 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
@ -83,8 +83,9 @@ chunk.
Compute */chunk commands: :h4
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
The following computes operate on chunks of atoms to produce per-chunk
values. Any compute whose style name ends in "/chunk" is in this
category:
"compute com/chunk"_compute_com_chunk.html
"compute gyration/chunk"_compute_gyration_chunk.html
@ -111,8 +112,8 @@ of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:
output, wih one or more values per chunk. The output can be used in
various ways:
As input to the "fix ave/time"_fix_ave_time.html command, which can
write the values to a file and optionally time average them. :ulb,l
@ -122,9 +123,27 @@ histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates. :l
As input to special functions of "equal-style
variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l
:ule
variables"_variable.html, like sum() and max() and ave(). E.g. to
find the largest cluster or fastest diffusing molecule or average
radius-of-gyration of a set of molecules (chunks). :l,ule
Other chunk commands: :h4
"compute chunk/spread/atom"_compute_chunk_spread_atom.html
"compute reduce/chunk"_compute_reduce_chunk.html :ul
The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
spreads per-chunk values to each atom in the chunk, producing per-atom
values as its output. This can be useful for outputting per-chunk
values to a per-atom "dump file"_dump.html. Or for using an atom's
associated chunk value in an "atom-style variable"_variable.html.
The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
peratom value across the atoms in each chunk to produce a value per
chunk. When used with the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command it can
create peratom values that induce a new set of chunks with a second
"compute chunk/atom"_compute_chunk_atom.html command.
Example calculations with chunks :h4
@ -164,3 +183,13 @@ compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
(6) An example of using a per-chunk value to apply per-atom forces to
compress individual polymer chains (molecules) in a mixture, is
explained on the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
(7) An example of using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the "compute
chunk/reduce"_compute_reduce_chunk.html command doc page.

131
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@ -0,0 +1,131 @@
"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Using LAMMPS in client/server mode :h3
Client/server coupling of two codes is where one code is the "client"
and sends request messages to a "server" code. The server responds to
each request with a reply message. This enables the two codes to work
in tandem to perform a simulation. LAMMPS can act as either a client
or server code.
Some advantages of client/server coupling are that the two codes run
as stand-alone executables; they are not linked together. Thus
neither code needs to have a library interface. This often makes it
easier to run the two codes on different numbers of processors. If a
message protocol (format and content) is defined for a particular kind
of simulation, then in principle any code that implements the
client-side protocol can be used in tandem with any code that
implements the server-side protocol, without the two codes needing to
know anything more specific about each other.
A simple example of client/server coupling is where LAMMPS is the
client code performing MD timestepping. Each timestep it sends a
message to a server quantum code containing current coords of all the
atoms. The quantum code computes energy and forces based on the
coords. It returns them as a message to LAMMPS, which completes the
timestep.
Alternate methods for code coupling with LAMMPS are described on
the "Howto couple"_Howto_couple.html doc page.
LAMMPS support for client/server coupling is in its "MESSAGE
package"_Packages_details.html#PKG-MESSAGE which implements several
commands that enable LAMMPS to act as a client or server, as discussed
below. The MESSAGE package also wraps a client/server library called
CSlib which enables two codes to exchange messages in different ways,
either via files, sockets, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. The CSlib has its own
"website"_http://cslib.sandia.gov with documentation and test
programs.
NOTE: For client/server coupling to work between LAMMPS and another
code, the other code also has to use the CSlib. This can sometimes be
done without any modifications to the other code by simply wrapping it
with a Python script that exchanges CSlib messages with LAMMPS and
prepares input for or processes output from the other code. The other
code also has to implement a matching protocol for the format and
content of messages that LAMMPS exchanges with it.
These are the commands currently in the MESSAGE package for two
protocols, MD and MC (Monte Carlo). New protocols can easily be
defined and added to this directory, where LAMMPS acts as either the
client or server.
"message"_message.html
"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
"server md"_server_md.html = LAMMPS is a server for computing MD forces
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
The server doc files give details of the message protocols
for data that is exchanged bewteen the client and server.
These example directories illustrate how to use LAMMPS as either a
client or server code:
examples/message
examples/COUPLE/README
examples/COUPLE/lammps_mc
examples/COUPLE/lammps_vasp :ul
The examples/message dir couples a client instance of LAMMPS to a
server instance of LAMMPS.
The lammps_mc dir shows how to couple LAMMPS as a server to a simple
Monte Carlo client code as the driver.
The lammps_vasp dir shows how to couple LAMMPS as a client code
running MD timestepping to VASP acting as a server providing quantum
DFT forces, thru a Python wrapper script on VASP.
Here is how to launch a client and server code together for any of the
4 modes of message exchange that the "message"_message.html command
and the CSlib support. Here LAMMPS is used as both the client and
server code. Another code could be subsitituted for either.
The examples below show launching both codes from the same window (or
batch script), using the "&" character to launch the first code in the
background. For all modes except {mpi/one}, you could also launch the
codes in separate windows on your desktop machine. It does not
matter whether you launch the client or server first.
In these examples either code can be run on one or more processors.
If running in a non-MPI mode (file or zmq) you can launch a code on a
single processor without using mpirun.
IMPORTANT: If you run in mpi/two mode, you must launch both codes via
mpirun, even if one or both of them runs on a single processor. This
is so that MPI can figure out how to connect both MPI processes
together to exchange MPI messages between them.
For message exchange in {file}, {zmq}, or {mpi/two} modes:
% mpirun -np 1 lmp_mpi -log log.client < in.client &
% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
% mpirun -np 4 lmp_mpi -log log.client < in.client &
% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
% mpirun -np 2 lmp_mpi -log log.client < in.client &
% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
For message exchange in {mpi/one} mode:
Launch both codes in a single mpirun command:
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre
The two -np values determine how many procs the client and the server
run on.
A LAMMPS executable run in this manner must use the -mpicolor color
command-line option as their its option, where color is an integer
label that will be used to distinguish one executable from another in
the multiple executables that the mpirun command launches. In this
example the client was colored with a 0, and the server with a 1.

14
doc/src/Howto_couple.txt
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@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
LAMMPS can be coupled to other codes in at least 3 ways. Each has
LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
:line
(1) Define a new "fix"_fix.html command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
@ -32,6 +34,8 @@ LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
:line
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
@ -52,6 +56,8 @@ command writes and reads.
See the "Modify command"_Modify_command.html doc page for info on how
to add a new command to LAMMPS.
:line
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
@ -102,3 +108,9 @@ on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
:line
(4) Couple LAMMPS with another code in a client/server mode. This is
described on the "Howto client/server"_Howto_client_server.html doc
page.

11
doc/src/Howto_nemd.txt
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@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the "fix flow/gauss"_fix_flow_gauss.html command.
:line
:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

11
doc/src/Howto_thermostat.txt
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@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
custom"_thermo_style.html command. Or you can use the
"thermo_modify"_thermo_modify.html command to re-define what
temperature compute is used for default thermodynamic output.
:line
:link(Daivis-thermostat)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

11
doc/src/Howto_viscosity.txt
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@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
command, which determines grad(Vstream) in the equation above.
@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
:line
:link(Daivis-viscosity)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

6
doc/src/Install_tarball.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Download source as a tarball :h3
Download source and documentation as a tarball :h3
You can download a current LAMMPS tarball from the "download page"_download
of the "LAMMPS website"_lws.
@ -22,6 +22,10 @@ few times per year, and undergo more testing before release. Patch
releases occur a couple times per month. The new contents in all
releases are listed on the "bug and feature page"_bug of the website.
Both tarballs include LAMMPS documentation (HTML and PDF files)
corresponding to that version. The download page also has an option
to download the current-version LAMMPS documentation by itself.
Older versions of LAMMPS can also be downloaded from "this
page"_older.

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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="22 Aug 2018 version">
<META NAME="docnumber" CONTENT="18 Sep 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>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
22 Aug 2018 version :c,h2
18 Sep 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

86
doc/src/Packages_details.txt
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@ -46,6 +46,7 @@ as contained in the file name.
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
"MEAM"_#PKG-MEAM,
"MESSAGE"_#PKG-MESSAGE,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
"MPIIO"_#PKG-MPIIO,
@ -88,10 +89,12 @@ as contained in the file name.
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
"USER-PHONON"_#PKG-USER-PHONON,
"USER-PTM"_#PKG-USER-PTM,
"USER-QMMM"_#PKG-USER-QMMM,
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@ -549,10 +552,6 @@ This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
extras"_Build_extras.html doc page.
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
the other on your system.
[Supporting info:]
src/MEAM: filenames -> commands
@ -563,6 +562,31 @@ examples/meam :ul
:line
MESSAGE package :link(PKG-MESSAGE),h4
[Contents:]
Commands to use LAMMPS as either a client or server and couple it to
another application.
[Install:]
This package has "specific installation
instructions"_Build_extras.html#message on the "Build
extras"_Build_extras.html doc page.
[Supporting info:]
src/MESSAGE: filenames -> commands
lib/message/README
"message"_message.html
"fix client/md"_fix_client_md.html
"server md"_server_md.html
"server mc"_server_mc.html
examples/message :ul
:line
MISC package :link(PKG-MISC),h4
[Contents:]
@ -1721,6 +1745,25 @@ examples/USER/phonon :ul
:line
USER-PTM package :link(PKG-USER-PTM),h4
[Contents:]
A "compute ptm/atom"_compute_ptm.html command that calculates
local structure characterization using the Polyhedral Template
Matching methodology.
[Author:] Peter Mahler Larsen (MIT).
[Supporting info:]
src/USER-PHONON: filenames -> commands
src/USER-PHONON/README
"fix phonon"_fix_phonon.html
examples/USER/phonon :ul
:line
USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
@ -1838,6 +1881,41 @@ examples/reax :ul
:line
USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
[Contents:]
A KSpace style which wraps the "ScaFaCoS Coulomb solver
library"_http://www.scafacos.de to compute long-range Coulombic
interactions.
To use this package you must have the ScaFaCoS library available on
your system.
[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
ScaFaCoS itself was developed by a consortium of German research
facilities with a BMBF (German Ministry of Science and Education)
funded project in 2009-2012. Participants of the consortium were the
Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
the Forschungszentrum Juelich.
[Install:]
This package has "specific installation
instructions"_Build_extras.html#user-scafacos on the "Build
extras"_Build_extras.html doc page.
[Supporting info:]
src/USER-SCAFACOS: filenames -> commands
src/USER-SCAFACOS/README
"kspace_style scafacos"_kspace_style.html
"kspace_modify"_kspace_modify.html
examples/USER/scafacos :ul
:line
USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]

1
doc/src/Packages_standard.txt
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@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no

2
doc/src/Packages_user.txt
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@ -62,10 +62,12 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no

25
doc/src/Run_options.txt
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@ -18,6 +18,7 @@ letter abbreviation can be used:
"-i or -in"_#file
"-k or -kokkos"_#run-kokkos
"-l or -log"_#log
"-m or -mpicolor"_#mpicolor
"-nc or -nocite"_#nocite
"-pk or -package"_#package
"-p or -partition"_#partition
@ -175,6 +176,30 @@ Option -plog will override the name of the partition log files file.N.
:line
[-mpicolor] color :link(mpicolor)
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
command which also launches another executable(s) at the same time.
(The other executable could be LAMMPS as well.) The color is an
integer value which should be different for each executable (another
application may set this value in a different way). LAMMPS and the
other executable(s) perform an MPI_Comm_split() with their own colors
to shrink the MPI_COMM_WORLD communication to be the subset of
processors they are actually running on.
Currently, this is only used in LAMMPS to perform client/server
messaging with another application. LAMMPS can act as either a client
or server (or both). More details are given on the "Howto
client/server"_Howto_client_server.html doc page.
Specifically, this refers to the "mpi/one" mode of messaging provided
by the "message"_message.html command and the CSlib library LAMMPS
links with from the lib/message directory. See the
"message"_message.html command for more details.
:line
[-nocite] :link(nocite)
Disable writing the log.cite file which is normally written to list

21
doc/src/Speed_kokkos.txt
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@ -106,6 +106,11 @@ modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.
NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
backend (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. However, when running on CPUs, it
@ -122,6 +127,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
If the "newton"_newton.html command is used in the input
script, it can also override the Newton flag defaults.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomics, which
don't require duplication. The use of atomics can be forced by compiling
with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
Kokkos-enabled pair_styles support data duplication. Alternatively, full
neighbor lists avoid the need for duplication or atomics but require
more compute operations per atom. When using the Kokkos Serial backend
or the OpenMP backend with a single thread, no duplication or atomics are
used. For CUDA and half neighbor lists, the KOKKOS package always uses
atomics.
[Core and Thread Affinity:]
When using multi-threading, it is important for performance to bind

4
doc/src/commands_list.txt
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@ -56,6 +56,7 @@ Commands :h1
lattice
log
mass
message
min_modify
min_style
minimize
@ -87,6 +88,9 @@ Commands :h1
restart
run
run_style
server
server_mc
server_md
set
shell
special_bonds

2
doc/src/compute.txt
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@ -183,6 +183,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"com"_compute_com.html - center-of-mass of group of atoms
@ -225,6 +226,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"slice"_compute_slice.html - extract values from global vector or array

66
doc/src/compute_angle_local.txt
View File

@ -10,20 +10,27 @@ compute angle/local command :h3
[Syntax:]
compute ID group-ID angle/local value1 value2 ... :pre
compute ID group-ID angle/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
angle/local = style name of this compute command :l
one or more values may be appended :l
value = {theta} or {eng} :l
value = {theta} or {eng} or {v_name} :l
{theta} = tabulate angles
{eng} = tabulate angle energies :pre
{eng} = tabulate angle energies
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = theta name
theta = only currently allowed arg
name = name of variable to set with theta :pre
:ule
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local eng theta :pre
compute 1 all angle/local eng theta
compute 1 all angle/local theta v_cos set theta t :pre
[Description:]
@ -36,6 +43,47 @@ The value {theta} is the angle for the 3 atoms in the interaction.
The value {eng} is the interaction energy for the angle.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the angle theta. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle theta. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
Note that the value of theta for each angle which stored in the
internal variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every angle in the system
and output the statistics in various ways:
variable t internal 0.0
variable cos equal cos(v_t)
variable cossq equal cos(v_t)*cos(v_t) :pre
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, angle,
cosine(angle), cosine^2(angle) for every angle in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
@ -65,12 +113,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
number of values. The length of the vector or number of rows in the
array is the number of angles. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

69
doc/src/compute_bond_local.txt
View File

@ -10,12 +10,12 @@ compute bond/local command :h3
[Syntax:]
compute ID group-ID bond/local value1 value2 ... :pre
compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
bond/local = style name of this compute command :l
one or more values may be appended :l
value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l
value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
{dist} = bond distance
{engpot} = bond potential energy
{force} = bond force :pre
@ -23,13 +23,22 @@ value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {
{engrot} = bond kinetic energy of rotation
{engtrans} = bond kinetic energy of translation
{omega} = magnitude of bond angular velocity
{velvib} = vibrational velocity along the bond length :pre
{velvib} = vibrational velocity along the bond length
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = dist name
dist = only currently allowed arg
name = name of variable to set with distance (dist) :pre
:ule
:ule
[Examples:]
compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force :pre
compute 1 all angle/local dist v_distsq set dist d :pre
[Description:]
@ -38,6 +47,10 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified by the
group parameter as explained below.
All these properties are computed for the pair of atoms in a bond,
whether the 2 atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value {dist} is the current length of the bond.
The value {engpot} is the potential energy for the bond,
@ -79,9 +92,41 @@ two atoms in the bond towards each other. A negative value means the
2 atoms are moving toward each other; a positive value means they are
moving apart.
Note that all these properties are computed for the pair of atoms in a
bond, whether the 2 atoms represent a simple diatomic molecule, or are
part of some larger molecule.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the bond distance. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the bond distance. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
As an example, these commands can be added to the bench/in.rhodo
script to compute the distance^2 of every bond in the system and
output the statistics in various ways:
variable d internal 0.0
variable dsq equal v_d*v_d :pre
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, distance,
distance^2 for every bond in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the distance^2 values and write them to a file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
@ -111,12 +156,12 @@ dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
number of values. The length of the vector or number of rows in the
array is the number of bonds. If a single value is specified, a local
vector is produced. If two or more values are specified, a local
array is produced where the number of columns = the number of values.
The vector or array can be accessed by any command that uses local
values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

11
doc/src/compute_chunk_atom.txt
View File

@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/atom = style name of this compute command :l
style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable}
style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name
{bin/1d} args = dim origin delta
dim = {x} or {y} or {z}
origin = {lower} or {center} or {upper} or coordinate value (distance units)
@ -40,7 +40,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
ncbin = # of concentric circle bins between rmin and rmax
{type} args = none
{molecule} args = none
{compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args
c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@ -85,7 +85,8 @@ compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes
compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes
compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes :pre
compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes
compute 1 all chunk/atom c_cluster :pre
[Description:]
@ -386,8 +387,8 @@ described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
compute/fix/variable value) may have been > {Nc}, because of the
compression operation.
compute/fix/variable) may have been > {Nc}, because of the compression
operation.
If {compress yes} is set, and the {compress} keyword comes after the
{limit} keyword, then the {limit} value of {Nc} is applied first to

174
doc/src/compute_chunk_spread_atom.txt Normal file
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@ -0,0 +1,174 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute chunk/spread/atom command :h3
[Syntax:]
compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/spread/atom = style name of this compute command :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
one or more inputs can be listed :l
input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l
c_ID = global vector calculated by a compute with ID
c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID
f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre
:ule
[Examples:]
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
[Description:]
Define a calculation that "spreads" one or more per-chunk values to
each atom in the chunk. This can be useful for creating a "dump
file"_dump.html where each atom lists info about the chunk it is in,
e.g. for post-processing purposes. It can also be used in "atom-style
variables"_variable.html that need info about the chunk each atom is
in. Examples are given below.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
For inputs that are computes, they must be a compute that calculates
per-chunk values. These are computes whose style names end in
"/chunk".
For inputs that are fixes, they should be a a fix that calculates
per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or
"fix ave/time"_fix_ave_time.html (assuming it is time-averaging
per-chunk data).
For each atom, this compute accesses its chunk ID from the specified
{chunkID} compute, then accesses the per-chunk value in each input.
Those values are copied to this compute to become the output for that
atom.
The values generated by this compute will be 0.0 for atoms not in the
specified compute group {group-ID}. They will also be 0.0 if the atom
is not in a chunk, as assigned by the {chunkID} compute. They will
also be 0.0 if the current chunk ID for the atom is out-of-bounds with
respect to the number of chunks stored by a particular input compute
or fix.
NOTE: LAMMPS does not check that a compute or fix which calculates
per-chunk values uses the same definition of chunks as this compute.
It's up to you to be consistent. Likewise, for a fix input, LAMMPS
does not check that it is per-chunk data. It only checks that the fix
produces a global vector or array.
:line
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
columns in the array, then an asterisk with no numeric values means
all indices from 1 to N. A leading asterisk means all indices from 1
to n (inclusive). A trailing asterisk means all indices from n to N
(inclusive). A middle asterisk means all indices from m to n
(inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute chunk/spread/atom
commands are equivalent, since the "compute
com/chunk"_compute_com_chunk.html command creates a per-atom array
with 3 columns:
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com\[*\]
compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre
:line
Here is an example of writing a dump file the with the center-of-mass
(COM) for the chunk each atom is in. The commands below can be added
to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
compute comchunk all chunk/spread/atom cmol c_com[*]
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify 1 sort id :pre
The same per-chunk data for each atom could be used to define per-atom
forces for the "fix addforce"_fix_addforce.html command. In this
example the forces act to pull atoms of an extended polymer chain
towards its COM in an attractive manner.
compute prop all property/atom xu yu zu
variable k equal 0.1
variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\])
variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\])
variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\])
fix 3 all addforce v_fx v_fy v_fz :pre
Note that "compute property/atom"_compute_property_atom.html is used
to generate unwrapped coordinates for use in the per-atom force
calculation, so that the effect of periodic boundaries is accounted
for properly.
Over time this applied force could shrink each polymer chain's radius
of gyration in a polymer mixture simulation. Here is output from the
bench/in.chain script. Thermo output is shown for 1000 steps, where
the last column is the average radius of gyration over all 320 chains
in the 32000 atom system:
compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
thermo_style custom step etotal press v_ave :pre
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362 :pre
:line
[Output info:]
This compute calculates a per-atom vector or array, which can be
accessed by any command that uses per-atom values from a compute as
input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The output is a per-atom vector if a single input value is specified,
otherwise a per-atom array is output. The number of columns in the
array is the number of inputs provided. The per-atom values for the
vector or each column of the array will be in whatever
"units"_units.html the corresponding input value is in.
The vector or array values are "intensive".
[Restrictions:] none
[Related commands:]
"compute chunk/atom"_compute_chunk_atom.html, "fix
ave/chunk"_fix_ave_chunk.html, "compute
reduce/chunk"_compute_reduce_chunk.html
[Default:] none

64
doc/src/compute_dihedral_local.txt
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@ -10,18 +10,25 @@ compute dihedral/local command :h3
[Syntax:]
compute ID group-ID dihedral/local value1 value2 ... :pre
compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
dihedral/local = style name of this compute command :l
one or more values may be appended :l
value = {phi} :l
{phi} = tabulate dihedral angles :pre
value = {phi} or {v_name} :l
{phi} = tabulate dihedral angles
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = phi name
phi = only currently allowed arg
name = name of variable to set with phi :pre
:ule
[Examples:]
compute 1 all dihedral/local phi :pre
compute 1 all dihedral/local phi v_cos set phi p :pre
[Description:]
@ -33,6 +40,47 @@ by the group parameter as explained below.
The value {phi} is the dihedral angle, as defined in the diagram on
the "dihedral_style"_dihedral_style.html doc page.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the dihedral angle phi. The
{name} specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle phi. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with phi.
Note that the value of phi for each angle which stored in the internal
variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every dihedral angle in
the system and output the statistics in various ways:
variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)*cos(v_p) :pre
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the angle,
cosine(angle), cosine^2(angle) for every dihedral in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
@ -57,12 +105,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
number of values. The length of the vector or number of rows in the
array is the number of dihedrals. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

121
doc/src/compute_ptm_atom.txt Normal file
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@ -0,0 +1,121 @@
"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
compute ptm/atom command :h3
[Syntax:]
compute ID group-ID ptm/atom structures threshold :pre
ID, group-ID are documented in "compute"_compute.html command
ptm/atom = style name of this compute command
structures = structure types to search for
threshold = lattice distortion threshold (RMSD) :ul
[Examples:]
compute 1 all ptm/atom default 0.1
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
compute 1 all ptm/atom all 0 :pre
[Description:]
Define a computation that determines the local lattice structure
around an atom using the PTM (Polyhedral Template Matching) method.
The PTM method is described in "(Larsen)"_#Larsen.
Currently, there are seven lattice structures PTM recognizes:
fcc = 1
hcp = 2
bcc = 3
ico (icosahedral) = 4
sc (simple cubic) = 5
dcub (diamond cubic) = 6
dhex (diamond hexagonal) = 7
other = 8 :ul
The value of the PTM structure will be 0 for atoms not in the specified
compute group. The choice of structures to search for can be specified using the "structures"
argument, which is a hyphen-separated list of structure keywords.
Two convenient pre-set options are provided:
default: fcc-hcp-bcc-ico
all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
The 'default' setting detects the same structures as the Common Neighbor Analysis method.
The 'all' setting searches for all structure types. A small performance penalty is
incurred for the diamond structures, so it is not recommended to use this option if
it is known that the simulation does not contain diamond structures.
PTM identifies structures using two steps. First, a graph isomorphism test is used
to identify potential structure matches. Next, the deviation is computed between the
local structure (in the simulation) and a template of the ideal lattice structure.
The deviation is calculated as:
:c,image(Eqs/ptm_rmsd.jpg)
Here, u and v contain the coordinates of the local and ideal structures respectively,
s is a scale factor, and Q is a rotation. The best match is identified by the
lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
points.
The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
a local structure is identified as disordered. Typical values are in the range 0.1-0.15,
but larger values may be desirable at higher temperatures.
A value of 0 is equivalent to infinity and can be used if no threshold is desired.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (e.g. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
{ptm/atom} style.
[Output info:]
This compute calculates a per-atom array, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
Results are stored in the per-atom array in the following order:
type
rmsd
interatomic distance
qw
qx
qy
qw :ul
The type is a number from 0 to 8. The rmsd is a positive real number.
The interatomic distance is computed from the scale factor in the RMSD equation.
The (qw,qx,qy,qz) parameters represent the orientation of the local structure
in quaternion form. The reference coordinates for each template (from which the
orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
[Restrictions:]
This fix is part of the USER-PTM package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"compute centro/atom"_compute_centro_atom.html
"compute cna/atom"_compute_cna_atom.html
[Default:] none
:line
:link(Larsen)
[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).

6
doc/src/compute_reduce.txt
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@ -97,9 +97,9 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html
command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL
compute 2 all reduce min myPress\[*\]
compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] &
myPress\[4\] myPress\[5\] myPress\[6\] :pre
compute 2 all reduce min c_myPress\[*\]
compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] &
c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre
:line

177
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@ -0,0 +1,177 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute reduce/chunk command :h3
[Syntax:]
compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
reduce/chunk = style name of this compute command :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
mode = {sum} or {min} or {max} :l
one or more inputs can be listed :l
input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name :pre
:ule
[Examples:]
compute 1 all reduce/chunk/atom mychunk min c_cluster :pre
[Description:]
Define a calculation that reduces one or more per-atom vectors into
per-chunk values. This can be useful for diagnostic output. Or when
used in conjunction with the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command it can be
used ot create per-atom values that induce a new set of chunks with a
second "compute chunk/atom"_compute_chunk_atom.html command. An
example is given below.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
For each atom, this compute accesses its chunk ID from the specified
{chunkID} compute. The per-atom value from an input contributes
to a per-chunk value corresponding the the chunk ID.
The reduction operation is specified by the {mode} setting and is
performed over all the per-atom values from the atoms in each chunk.
The {sum} option adds the pre-atom values to a per-chunk total. The
{min} or {max} options find the minimum or maximum value of the
per-atom values for each chunk.
Note that only atoms in the specified group contribute to the
reduction operation. If the {chunkID} compute returns a 0 for the
chunk ID of an atom (i.e. the atom is not in a chunk defined by the
"compute chunk/atom"_compute_chunk_atom.html command), that atom will
also not contribute to the reduction operation. An input that is a
compute or fix may define its own group which affects the quantities
it returns. For example, a compute with return a zero value for atoms
that are not in the group specified for that compute.
Each listed input is operated on independently. Each input can be the
result of a "compute"_compute.html or "fix"_fix.html or the evaluation
of an atom-style "variable"_variable.html.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "*" or "*n" or "n*" or
"m*n". If N = the size of the vector (for {mode} = scalar) or the
number of columns in the array (for {mode} = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute reduce/chunk
commands are equivalent, since the "compute
property/chunk"_compute_property_chunk.html command creates a per-atom
array with 3 columns:
compute prop all property/atom vx vy vz
compute 10 all reduce/chunk mychunk max c_prop\[*\]
compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre
:line
Here is an example of using this compute, in conjunction with the
compute chunk/spread/atom command to identify self-assembled micelles.
The commands below can be added to the examples/in.micelle script.
Imagine a collection of polymer chains or small molecules with
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
to a group called "phobic".
These commands will assign a unique cluster ID to all HP atoms within
a specified distance of each other. A cluster will contain all HP
atoms in a single molecule, but also the HP atoms in nearby molecules,
e.g. molecules that have clumped to form a micelle due to the
attraction induced by the hydrophobicity. The output of the
chunk/reduce command will be a cluster ID per chunk (molecule).
Molecules with the same cluster ID are in the same micelle.
group phobic type 4 # specific to in.micelle model
compute cluster phobic cluster/atom 2.0
compute cmol all chunk/atom molecule
compute reduce phobic reduce/chunk cmol min c_cluster :pre
This per-chunk info could be output in at least two ways:
fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre
compute spread all chunk/spread/atom cmol c_reduce
dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread
dump_modify 1 sort id :pre
In the first case, each snapshot in the tmp.phobic file will contain
one line per molecule. Molecules with the same value are in the same
micelle. In the second case each dump snapshot contains all atoms,
each with a final field with the cluster ID of the micelle that the HP
atoms of that atom's molecule belong to.
The result from compute chunk/spread/atom can be used to define a new
set of chunks, where all the atoms in all the molecules in the same
micelle are assigned to the same chunk, i.e. one chunk per micelle.
compute micelle all chunk/atom c_spread compress yes :pre
Further analysis on a per-micelle basis can now be performed using any
of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html
doc page. E.g. count the number of atoms in each micelle, calculate
its center or mass, shape (moments of intertia), radius of gyration,
etc.
compute prop all property/chunk micelle count
fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre
Each snapshot in the tmp.micelle file will have one line per micelle
with its count of atoms, plus a first line for a chunk with all the
solvent atoms. By the time 50000 steps have elapsed there are a
handful of large micelles.
:line
[Output info:]
This compute calculates a global vector if a single input value is
specified, otherwise a global array is output. The number of columns
in the array is the number of inputs provided. The length of the
vector or the number of vector elements or array rows = the number of
chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The vector or array can
be accessed by any command that uses global values from a compute as
input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The per-atom values for the vector or each column of the array will be
in whatever "units"_units.html the corresponding input value is in.
The vector or array values are "intensive".
[Restrictions:] none
[Related commands:]
"compute chunk/atom"_compute_chunk_atom.html, "compute
reduce"_compute_reduce.html, "compute
chunk/spread/atom"_compute_chunk_spread_atom.html
[Default:] none

111
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@ -0,0 +1,111 @@
"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
compute stress/mop command :h3
compute stress/mop/profile command :h3
[Syntax:]
compute ID group-ID style dir args keywords ... :pre
ID, group-ID are documented in "compute"_compute.html command
style = {stress/mop} or {stress/mop/profile}
dir = {x} or {y} or {z} is the direction normal to the plane
args = argument specific to the compute style
keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
{stress/mop} args = pos
pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
{stress/mop/profile} args = origin delta
origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
delta = value (distance units) is the distance between planes :pre
compute 1 all stress/mop x lower total
compute 1 liquid stress/mop z 0.0 kin conf
fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
compute 1 all stress/mop/profile x lower 0.1 total
compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf
fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
[Description:]
Compute {stress/mop} and compute {stress/mop/profile} define computations that
calculate components of the local stress tensor using the method of
planes "(Todd)"_#mop-todd. Specifically in compute {stress/mop} calculates 3
components are computed in directions {dir},{x}; {dir},{y}; and
{dir},{z}; where {dir} is the direction normal to the plane, while
in compute {stress/mop/profile} the profile of the stress is computed.
Contrary to methods based on histograms of atomic stress (i.e. using
"compute stress/atom"_compute_stress_atom.html), the method of planes is
compatible with mechanical balance in heterogeneous systems and at
interfaces "(Todd)"_#mop-todd.
The stress tensor is the sum of a kinetic term and a configurational
term, which are given respectively by Eq. (21) and Eq. (16) in
"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
atoms have crossed the plane if their positions at times t-dt and t are
one on either side of the plane, and uses the velocity at time t-dt/2
given by the velocity-Verlet algorithm.
Between one and three keywords can be used to indicate which
contributions to the stress must be computed: kinetic stress (kin),
configurational stress (conf), and/or total stress (total).
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the pressure added by the "pair_modify tail
yes"_pair_modify.html command, since those are contributions to the global system pressure.
[Output info:]
Compute {stress/mop} calculates a global vector (indices starting at 1), with 3
values for each declared keyword (in the order the keywords have been
declared). For each keyword, the stress tensor components are ordered as
follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute {stress/mop/profile} instead calculates a global array, with 1 column
giving the position of the planes where the stress tensor was computed,
and with 3 columns of values for each declared keyword (in the order the
keywords have been declared). For each keyword, the profiles of stress
tensor components are ordered as follows: stress_dir,x; stress_dir,y;
and stress_dir,z.
The values are in pressure "units"_units.html.
The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
[Restrictions:]
These styles are part of the USER-MISC package. They are only enabled if
LAMMPS is built with that package. See the "Build package"_Build_package.html
doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method pair->single() to be implemented. In
particular, it does not work with more than two-body pair interactions,
intra-molecular interactions, and long range (kspace) interactions.
[Related commands:]
"compute stress/atom"_compute_stress_atom.html
[Default:] none
:line
:link(mop-todd)
[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
Phys. Rev. E 52, 1627 (1995).

4
doc/src/computes.txt
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@ -15,6 +15,7 @@ Computes :h1
compute_bond_local
compute_centro_atom
compute_chunk_atom
compute_chunk_spread_atom
compute_cluster_atom
compute_cna_atom
compute_cnp_atom
@ -70,8 +71,10 @@ Computes :h1
compute_property_atom
compute_property_chunk
compute_property_local
compute_ptm_atom
compute_rdf
compute_reduce
compute_reduce_chunk
compute_rigid_local
compute_saed
compute_slice
@ -98,6 +101,7 @@ Computes :h1
compute_sna_atom
compute_spin
compute_stress_atom
compute_stress_mop
compute_tally
compute_tdpd_cc_atom
compute_temp

4
doc/src/fix_box_relax.txt
View File

@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those
of the reference dimensions. If this is not the case, then the
converged stress tensor will not equal that specified by the user. We
can resolve this problem by periodically resetting the reference
dimensions. The keyword {nreset_ref} controls how often this is done.
If this keyword is not used, or is given a value of zero, then the
dimensions. The keyword {nreset} controls how often this is done. If
this keyword is not used, or is given a value of zero, then the
reference dimensions are set to those of the initial simulation domain
and are never changed. A value of {nstep} means that every {nstep}
minimization steps, the reference dimensions are set to those of the

106
doc/src/fix_client_md.txt Normal file
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@ -0,0 +1,106 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix client/md command :h3
[Syntax:]
fix ID group-ID client/md :pre
ID, group-ID are documented in "fix"_fix.html command
client/md = style name of this fix command :ul
[Examples:]
fix 1 all client/md :pre
[Description:]
This fix style enables LAMMPS to run as a "client" code and
communicate each timestep with a separate "server" code to perform an
MD simulation together.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When using this fix, LAMMPS (as the client code) passes the current
coordinates of all particles to the server code each timestep, which
computes their interaction, and returns the energy, forces, and virial
for the interacting particles to LAMMPS, so it can complete the
timestep.
The server code could be a quantum code, or another classical MD code
which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
does not have. In the quantum case, this fix is a mechanism for
running {ab initio} MD with quantum forces.
The group associated with this fix is ignored.
The protocol and "units"_units.html for message format and content
that LAMMPS exchanges with the server code is defined on the "server
md"_server_md.html doc page.
Note that when using LAMMPS as an MD client, your LAMMPS input script
should not normally contain force field commands, like a
"pair_style"_pair_style.html, "bond_style"_bond_style.html, or
"kspace_style"_kspace_style.html commmand. However it is possible for
a server code to only compute a portion of the full force-field, while
LAMMPS computes the remaining part. Your LAMMPS script can also
specify boundary conditions or force constraints in the usual way,
which will be added to the per-atom forces returned by the server
code.
See the examples/message dir for example scripts where LAMMPS is both
the "client" and/or "server" code for this kind of client/server MD
simulation. The examples/message/README file explains how to launch
LAMMPS and another code in tandem to perform a coupled simulation.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential energy computed by the server application to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The "fix_modify"_fix_modify.html {virial} option is supported by this
fix to add the server application's contribution to the system's
virial as part of "thermodynamic output"_thermo_style.html. The
default is {virial yes}
This fix computes a global scalar which can be accessed by various
"output commands"_Howto_output.html. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
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 MESSAGE package. It is only enabled if LAMMPS
was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
the other server code.
[Related commands:]
"message"_message.html, "server"_server.html
[Default:] none

9
doc/src/fix_nvt_sllod.txt
View File

@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the "fix nvt"_fix_nh.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
command. See, for example, discussion of the {temp} and {drag}
@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.
:link(Daivis)
[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).
:link(Daivis-sllod)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

6
doc/src/fix_shake.txt
View File

@ -214,8 +214,10 @@ which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
(e.g. linear CO2 molecule). This causes numeric difficulties.
SHAKE or RATTLE should not be used to constrain an angle at 180
degrees (e.g. linear CO2 molecule). This causes numeric difficulties.
You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to
make a linear molecule rigid.
[Related commands:] none

1
doc/src/fixes.txt
View File

@ -26,6 +26,7 @@ Fixes :h1
fix_bond_swap
fix_bond_react
fix_box_relax
fix_client_md
fix_cmap
fix_colvars
fix_controller

471
doc/src/kspace_modify.txt
View File

@ -13,47 +13,53 @@ kspace_modify command :h3
kspace_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} or {disp/auto}:l
{mesh} value = x y z
x,y,z = grid size in each dimension for long-range Coulombics
{mesh/disp} value = x y z
x,y,z = grid size in each dimension for 1/r^6 dispersion
{order} value = N
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
{order/disp} value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid
{mix/disp} value = {pair} or {geom} or {none}
{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
{minorder} value = M
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} or {fftbench} or {force/disp/kspace} or {force/disp/real} or {force} or {gewald/disp} or {gewald} or {kmax/ewald} or {mesh} or {minorder} or {mix/disp} or {order/disp} or {order} or {overlap} or {scafacos} or {slab} or {splittol} :l
{collective} value = {yes} or {no}
{compute} value = {yes} or {no}
{cutoff/adjust} value = {yes} or {no}
{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
{disp/auto} value = yes or no
{fftbench} value = {yes} or {no}
{force/disp/real} value = accuracy (force units)
{force/disp/kspace} value = accuracy (force units)
{force} value = accuracy (force units)
{gewald} value = rinv (1/distance units)
rinv = G-ewald parameter for Coulombics
{gewald/disp} value = rinv (1/distance units)
rinv = G-ewald parameter for dispersion
{kmax/ewald} value = kx ky kz
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
{mesh} value = x y z
x,y,z = grid size in each dimension for long-range Coulombics
{mesh/disp} value = x y z
x,y,z = grid size in each dimension for 1/r^6 dispersion
{minorder} value = M
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
{mix/disp} value = {pair} or {geom} or {none}
{order} value = N
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
{order/disp} value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid
{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
{pressure/scalar} value = {yes} or {no}
{scafacos} values = option value1 value2 ...
option = {tolerance}
value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel}
option = {fmm_tuning}
value = {0} or {1}
{slab} value = volfactor or {nozforce}
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
{nozforce} turns off kspace forces in the z direction
{compute} value = {yes} or {no}
{cutoff/adjust} value = {yes} or {no}
{pressure/scalar} value = {yes} or {no}
{fftbench} value = {yes} or {no}
{collective} value = {yes} or {no}
{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
{kmax/ewald} value = kx ky kz
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
{force/disp/real} value = accuracy (force units)
{force/disp/kspace} value = accuracy (force units)
{splittol} value = tol
tol = relative size of two eigenvalues (see discussion below)
{disp/auto} value = yes or no :pre
tol = relative size of two eigenvalues (see discussion below) :pre
:ule
[Examples:]
kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0 :pre
kspace_modify slab 3.0
kspace_modify scafacos tolerance energy :pre
[Description:]
@ -61,6 +67,132 @@ Set parameters used by the kspace solvers defined by the
"kspace_style"_kspace_style.html command. Not all parameters are
relevant to all kspace styles.
:line
The {collective} keyword applies only to PPPM. It is set to {no} by
default, except on IBM BlueGene machines. If this option is set to
{yes}, LAMMPS will use MPI collective operations to remap data for
3d-FFT operations instead of the default point-to-point communication.
This is faster on IBM BlueGene machines, and may also be faster on
other machines if they have an efficient implementation of MPI
collective operations and adequate hardware.
:line
The {compute} keyword allows Kspace computations to be turned off,
even though a "kspace_style"_kspace_style.html is defined. This is
not useful for running a real simulation, but can be useful for
debugging purposes or for computing only partial forces that do not
include the Kspace contribution. You can also do this by simply not
defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
"pair_style"_pair_style.html requires a kspace style to be defined.
This keyword gives you that option.
:line
The {cutoff/adjust} keyword applies only to MSM. If this option is
turned on, the Coulombic cutoff will be automatically adjusted at the
beginning of the run to give the desired estimated error. Other
cutoffs such as LJ will not be affected. If the grid is not set using
the {mesh} command, this command will also attempt to use the optimal
grid that minimizes cost using an estimate given by
"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat
experimental, and still may not yield the optimal parameters.
:line
The {diff} keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The {ik} approach is the default for
PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It
performs differentiation in Kspace, and uses 3 FFTs to transfer each
component of the computed fields back to real space for total of 4
FFTs per timestep.
The analytic differentiation {ad} approach uses only 1 FFT to transfer
information back to real space for a total of 2 FFTs per timestep. It
then performs analytic differentiation on the single quantity to
generate the 3 components of the electric field at each grid point.
This is sometimes referred to as "smoothed" PPPM. This approach
requires a somewhat larger PPPM mesh to achieve the same accuracy as
the {ik} method. Currently, only the {ik} method (default) can be
used for a triclinic simulation cell with PPPM. The {ad} method is
always used for MSM.
NOTE: Currently, not all PPPM styles support the {ad} option. Support
for those PPPM variants will be added later.
:line
The {disp/auto} option controls whether the pppm/disp is allowed to
generate PPPM parameters automatically. If set to {no}, parameters have
to be specified using the {gewald/disp}, {mesh/disp},
{force/disp/real} or {force/disp/kspace} keywords, or
the code will stop with an error message. When this option is set to
{yes}, the error message will not appear and the simulation will start.
For a typical application, using the automatic parameter generation
will provide simulations that are either inaccurate or slow. Using this
option is thus not recommended. For guidelines on how to obtain good
parameters, see the "How-To"_Howto_dispersion.html discussion.
:line
The {fftbench} keyword applies only to PPPM. It is off by default. If
this option is turned on, LAMMPS will perform a short FFT benchmark
computation and report its timings, and will thus finish a some seconds
later than it would if this option were off.
:line
The {force/disp/real} and {force/disp/kspace} keywords set the force
accuracy for the real and space computations for the dispersion part
of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal
performance and accuracy in the results is obtained when these values
are different.
:line
The {force} keyword overrides the relative accuracy parameter set by
the "kspace_style"_kspace_style.html command with an absolute
accuracy. The accuracy determines the RMS error in per-atom forces
calculated by the long-range solver and is thus specified in force
units. A negative value for the accuracy setting means to use the
relative accuracy parameter. The accuracy setting is used in
conjunction with the pairwise cutoff to determine the number of
K-space vectors for style {ewald}, the FFT grid size for style
{pppm}, or the real space grid size for style {msm}.
:line
The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
parameter for charge as {rinv} in reciprocal distance units. Without
this setting, LAMMPS chooses the parameter automatically as a function
of cutoff, precision, grid spacing, etc. This means it can vary from
one simulation to the next which may not be desirable for matching a
KSpace solver to a pre-tabulated pairwise potential. This setting can
also be useful if Ewald or PPPM fails to choose a good grid spacing
and G-ewald parameter automatically. If the value is set to 0.0,
LAMMPS will choose the G-ewald parameter automatically. MSM does not
use the {gewald} parameter.
:line
The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
parameter for dispersion as {rinv} in reciprocal distance units. It
has the same meaning as the {gewald} setting for Coulombics.
:line
The {kmax/ewald} keyword sets the number of kspace vectors in each
dimension for kspace style {ewald}. The three values must be positive
integers, or else (0,0,0), which unsets the option. When this option
is not set, the Ewald sum scheme chooses its own kspace vectors,
consistent with the user-specified accuracy and pairwise cutoff. In
any case, if kspace style {ewald} is invoked, the values used are
printed to the screen and the log file at the start of the run.
:line
The {mesh} keyword sets the grid size for kspace style {pppm} or
{msm}. In the case of PPPM, this is the FFT mesh, and each dimension
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
@ -70,6 +202,8 @@ or MSM solver chooses its own grid size, consistent with the
user-specified accuracy and pairwise cutoff. Values for x,y,z of
0,0,0 unset the option.
:line
The {mesh/disp} keyword sets the grid size for kspace style
{pppm/disp}. This is the FFT mesh for long-range dispersion and ach
dimension must be factorizable into powers of 2, 3, and 5. When this
@ -77,39 +211,7 @@ option is not set, the PPPM solver chooses its own grid size,
consistent with the user-specified accuracy and pairwise cutoff.
Values for x,y,z of 0,0,0 unset the option.
The {order} keyword determines how many grid spacings an atom's charge
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
The default for this parameter is 5 for PPPM and 8 for MSM, which
means each charge spans 5 or 8 grid cells in each dimension,
respectively. For the LAMMPS implementation of MSM, the order can
range from 4 to 10 and must be even. For PPPM, the minimum allowed
setting is 2 and the maximum allowed setting is 7. The larger the
value of this parameter, the smaller that LAMMPS will set the grid
size, to achieve the requested accuracy. Conversely, the smaller the
order value, the larger the grid size will be. Note that there is an
inherent trade-off involved: a small grid will lower the cost of FFTs
or MSM direct sum, but a larger order parameter will increase the cost
of interpolating charge/fields to/from the grid.
The {order/disp} keyword determines how many grid spacings an atom's
dispersion term extends when it is mapped to the grid in kspace style
{pppm/disp}. It has the same meaning as the {order} setting for
Coulombics.
The {overlap} keyword can be used in conjunction with the {minorder}
keyword with the PPPM styles to adjust the amount of communication
that occurs when values on the FFT grid are exchanged between
processors. This communication is distinct from the communication
inherent in the parallel FFTs themselves, and is required because
processors interpolate charge and field values using grid point values
owned by neighboring processors (i.e. ghost point communication). If
the {overlap} keyword is set to {yes} then this communication is
allowed to extend beyond nearest-neighbor processors, e.g. when using
lots of processors on a small problem. If it is set to {no} then the
communication will be limited to nearest-neighbor processors and the
{order} setting will be reduced if necessary, as explained by the
{minorder} keyword discussion. The {overlap} keyword is always set to
{yes} in MSM.
:line
The {minorder} keyword allows LAMMPS to reduce the {order} setting if
necessary to keep the communication of ghost grid point limited to
@ -126,6 +228,42 @@ error if the grid communication is non-nearest-neighbor and {overlap}
is set to {no}. The {minorder} keyword is not currently supported in
MSM.
:line
The {mix/disp} keyword selects the mixing rule for the dispersion
coefficients. With {pair}, the dispersion coefficients of unlike
types are computed as indicated with "pair_modify"_pair_modify.html.
With {geom}, geometric mixing is enforced on the dispersion
coefficients in the kspace coefficients. When using the arithmetic
mixing rule, this will speed-up the simulations but introduces some
error in the force computations, as shown in "(Wennberg)"_#Wennberg.
With {none}, it is assumed that no mixing rule is
applicable. Splitting of the dispersion coefficients will be performed
as described in "(Isele-Holder)"_#Isele-Holder1.
This splitting can be influenced with the {splittol} keywords. Only
the eigenvalues that are larger than tol compared to the largest
eigenvalues are included. Using this keywords the original matrix of
dispersion coefficients is approximated. This leads to faster
computations, but the accuracy in the reciprocal space computations of
the dispersion part is decreased.
:line
The {order} keyword determines how many grid spacings an atom's charge
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
The default for this parameter is 5 for PPPM and 8 for MSM, which
means each charge spans 5 or 8 grid cells in each dimension,
respectively. For the LAMMPS implementation of MSM, the order can
range from 4 to 10 and must be even. For PPPM, the minimum allowed
setting is 2 and the maximum allowed setting is 7. The larger the
value of this parameter, the smaller that LAMMPS will set the grid
size, to achieve the requested accuracy. Conversely, the smaller the
order value, the larger the grid size will be. Note that there is an
inherent trade-off involved: a small grid will lower the cost of FFTs
or MSM direct sum, but a larger order parameter will increase the cost
of interpolating charge/fields to/from the grid.
The PPPM order parameter may be reset by LAMMPS when it sets up the
FFT grid if the implied grid stencil extends beyond the grid cells
owned by neighboring processors. Typically this will only occur when
@ -134,30 +272,102 @@ be generated indicating the order parameter is being reduced to allow
LAMMPS to run the problem. Automatic adjustment of the order parameter
is not supported in MSM.
The {force} keyword overrides the relative accuracy parameter set by
the "kspace_style"_kspace_style.html command with an absolute
accuracy. The accuracy determines the RMS error in per-atom forces
calculated by the long-range solver and is thus specified in force
units. A negative value for the accuracy setting means to use the
relative accuracy parameter. The accuracy setting is used in
conjunction with the pairwise cutoff to determine the number of
K-space vectors for style {ewald}, the FFT grid size for style
{pppm}, or the real space grid size for style {msm}.
:line
The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
parameter for charge as {rinv} in reciprocal distance units. Without
this setting, LAMMPS chooses the parameter automatically as a function
of cutoff, precision, grid spacing, etc. This means it can vary from
one simulation to the next which may not be desirable for matching a
KSpace solver to a pre-tabulated pairwise potential. This setting can
also be useful if Ewald or PPPM fails to choose a good grid spacing
and G-ewald parameter automatically. If the value is set to 0.0,
LAMMPS will choose the G-ewald parameter automatically. MSM does not
use the {gewald} parameter.
The {order/disp} keyword determines how many grid spacings an atom's
dispersion term extends when it is mapped to the grid in kspace style
{pppm/disp}. It has the same meaning as the {order} setting for
Coulombics.
The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
parameter for dispersion as {rinv} in reciprocal distance units. It
has the same meaning as the {gewald} setting for Coulombics.
:line
The {overlap} keyword can be used in conjunction with the {minorder}
keyword with the PPPM styles to adjust the amount of communication
that occurs when values on the FFT grid are exchanged between
processors. This communication is distinct from the communication
inherent in the parallel FFTs themselves, and is required because
processors interpolate charge and field values using grid point values
owned by neighboring processors (i.e. ghost point communication). If
the {overlap} keyword is set to {yes} then this communication is
allowed to extend beyond nearest-neighbor processors, e.g. when using
lots of processors on a small problem. If it is set to {no} then the
communication will be limited to nearest-neighbor processors and the
{order} setting will be reduced if necessary, as explained by the
{minorder} keyword discussion. The {overlap} keyword is always set to
{yes} in MSM.
:line
The {pressure/scalar} keyword applies only to MSM. If this option is
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
be computed, which can be used, for example, to run an isotropic barostat.
Computing the full pressure tensor with MSM is expensive, and this option
provides a faster alternative. The scalar pressure is computed using a
relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer
instead of using the virial equation. This option cannot be used to access
individual components of the pressure tensor, to compute per-atom virial,
or with suffix kspace/pair styles of MSM, like OMP or GPU.
:line
The {scafacos} keyword is used for settings that are passed to the
ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html.
The {tolerance} option affects how the {accuracy} specified with the
"kspace_style"_kspace_style.html command is interpreted by ScaFaCoS.
The following values may be used:
energy = absolute accuracy in total Coulomic energy
energy_rel = relative accuracy in total Coulomic energy
potential = absolute accuracy in total Coulomic potential
potential_rel = relative accuracy in total Coulomic potential
field = absolute accuracy in electric field
field_rel = relative accuracy in electric field :ul
The values with suffix _rel indicate the tolerance is a relative
tolerance; the other values impose an absolute tolerance on the given
quantity. Absoulte tolerance in this case means, that for a given
quantity q and a given absolute tolerance of t_a the result should
be between q-t_a and q+t_a. For a relative tolerance t_r the relative
error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r.
As a consequence of this, the tolerance type should be checked, when
performing computations with a high absolute field / energy. E.g.
if the total energy in the system is 1000000.0 an absolute tolerance
of 1e-3 would mean that the result has to be between 999999.999 and
1000000.001, which would be equivalent to a relative tolerance of
1e-9.
The energy and energy_rel values, set a tolerance based on the total
Coulomic energy of the system. The potential and potential_rel set a
tolerance based on the per-atom Coulomic energy. The field and
field_rel tolerance types set a tolerance based on the electric field
values computed by ScaFaCoS. Since per-atom forces are derived from
the per-atom electric field, this effectively sets a tolerance on the
forces, simimlar to other LAMMPS KSpace styles, as explained on the
"kspace_style"_kspace_style.html doc page.
Note that not all ScaFaCoS solvers support all tolerance types.
These are the allowed values for each method:
fmm = energy and energy_rel
p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
p3m = field
ewald = field
direct = has no tolerance tuning :ul
If the tolerance type is not changed, the default values for the
tolerance type are the first values in the above list, e.g. energy
is the default tolerance type for the fmm solver.
The {fmm_tuning} option is only relevant when using the FMM method.
It activates (value=1) or deactivates (value=0) an internal tuning
mechanism for the FMM solver. The tuning operation runs sequentially
and can be very time-consuming. Usually it is not needed for systems
with a homogenous charge distribution. The default for this option is
therefore {0}. The FMM internal tuning is performed once, when the
solver is set up.
:line
The {slab} keyword allows an Ewald or PPPM solver to be used for a
systems that are periodic in x,y but non-periodic in z - a
@ -191,92 +401,7 @@ the "fix efield"_fix_efield.html command, it will not give the correct
dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction
not being compatible with how "fix efield"_fix_efield.html works.
The {compute} keyword allows Kspace computations to be turned off,
even though a "kspace_style"_kspace_style.html is defined. This is
not useful for running a real simulation, but can be useful for
debugging purposes or for computing only partial forces that do not
include the Kspace contribution. You can also do this by simply not
defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
"pair_style"_pair_style.html requires a kspace style to be defined.
This keyword gives you that option.
The {cutoff/adjust} keyword applies only to MSM. If this option is
turned on, the Coulombic cutoff will be automatically adjusted at the
beginning of the run to give the desired estimated error. Other
cutoffs such as LJ will not be affected. If the grid is not set using
the {mesh} command, this command will also attempt to use the optimal
grid that minimizes cost using an estimate given by
"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat
experimental, and still may not yield the optimal parameters.
The {pressure/scalar} keyword applies only to MSM. If this option is
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
be computed, which can be used, for example, to run an isotropic barostat.
Computing the full pressure tensor with MSM is expensive, and this option
provides a faster alternative. The scalar pressure is computed using a
relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer
instead of using the virial equation. This option cannot be used to access
individual components of the pressure tensor, to compute per-atom virial,
or with suffix kspace/pair styles of MSM, like OMP or GPU.
The {fftbench} keyword applies only to PPPM. It is off by default. If
this option is turned on, LAMMPS will perform a short FFT benchmark
computation and report its timings, and will thus finish a some seconds
later than it would if this option were off.
The {collective} keyword applies only to PPPM. It is set to {no} by
default, except on IBM BlueGene machines. If this option is set to
{yes}, LAMMPS will use MPI collective operations to remap data for
3d-FFT operations instead of the default point-to-point communication.
This is faster on IBM BlueGene machines, and may also be faster on
other machines if they have an efficient implementation of MPI
collective operations and adequate hardware.
The {diff} keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The {ik} approach is the default for
PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It
performs differentiation in Kspace, and uses 3 FFTs to transfer each
component of the computed fields back to real space for total of 4
FFTs per timestep.
The analytic differentiation {ad} approach uses only 1 FFT to transfer
information back to real space for a total of 2 FFTs per timestep. It
then performs analytic differentiation on the single quantity to
generate the 3 components of the electric field at each grid point.
This is sometimes referred to as "smoothed" PPPM. This approach
requires a somewhat larger PPPM mesh to achieve the same accuracy as
the {ik} method. Currently, only the {ik} method (default) can be
used for a triclinic simulation cell with PPPM. The {ad} method is
always used for MSM.
NOTE: Currently, not all PPPM styles support the {ad} option. Support
for those PPPM variants will be added later.
The {kmax/ewald} keyword sets the number of kspace vectors in each
dimension for kspace style {ewald}. The three values must be positive
integers, or else (0,0,0), which unsets the option. When this option
is not set, the Ewald sum scheme chooses its own kspace vectors,
consistent with the user-specified accuracy and pairwise cutoff. In
any case, if kspace style {ewald} is invoked, the values used are
printed to the screen and the log file at the start of the run.
With the {mix/disp} keyword one can select the mixing rule for the
dispersion coefficients. With {pair}, the dispersion coefficients of
unlike types are computed as indicated with
"pair_modify"_pair_modify.html. With {geom}, geometric mixing is
enforced on the dispersion coefficients in the kspace
coefficients. When using the arithmetic mixing rule, this will
speed-up the simulations but introduces some error in the force
computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is
assumed that no mixing rule is applicable. Splitting of the dispersion
coefficients will be performed as described in
"(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with
the {splittol} keywords. Only the eigenvalues that are larger than tol
compared to the largest eigenvalues are included. Using this keywords
the original matrix of dispersion coefficients is approximated. This
leads to faster computations, but the accuracy in the reciprocal space
computations of the dispersion part is decreased.
:line
The {force/disp/real} and {force/disp/kspace} keywords set the force
accuracy for the real and space computations for the dispersion part
@ -295,6 +420,8 @@ provide simulations that are either inaccurate or slow. Using this
option is thus not recommended. For guidelines on how to obtain good
parameters, see the "Howto dispersion"_Howto_dispersion.html doc page.
:line
[Restrictions:] none
[Related commands:]
@ -306,10 +433,12 @@ parameters, see the "Howto dispersion"_Howto_dispersion.html doc page.
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
order/disp = 7.
yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff =
ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace
= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel,
order = order/disp = 7. For scafacos settings, the scafacos tolerance
option depends on the method chosen, as documented above. The
scafacos fmm_tuning default = 0.
:line

92
doc/src/kspace_style.txt
View File

@ -12,7 +12,7 @@ kspace_style command :h3
kspace_style style value :pre
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
{none} value = none
{ewald} value = accuracy
accuracy = desired relative error in forces
@ -22,7 +22,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{pppm} value = accuracy
accuracy = desired relative error in forces
{pppm/cg} value = accuracy (smallq)
{pppm/cg} values = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{pppm/disp} value = accuracy
@ -56,7 +56,10 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{msm/cg/omp} value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units) :pre
smallq = cutoff for charges to be considered (optional) (charge units)
{scafacos} values = method accuracy
method = fmm or p2nfft or ewald or direct
accuracy = desired relative error in forces :pre
:ule
[Examples:]
@ -64,6 +67,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace style msm 1.0e-4
kspace style scafacos fmm 1.0e-4
kspace_style none :pre
[Description:]
@ -211,6 +215,63 @@ pressure simulation with MSM will cause the code to run slower.
:line
The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
library"_http://www.scafacos.de which provides a variety of solver
methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012
gives an overview of ScaFaCoS.
ScaFaCoS was developed by a consortium of German research facilities
with a BMBF (German Ministry of Science and Education) funded project
in 2009-2012. Participants of the consortium were the Universities of
Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
Forschungszentrum Juelich.
The library is available for download at "http://scafacos.de" or can
be cloned from the git-repository
"git://github.com/scafacos/scafacos.git".
In order to use this KSpace style, you must download and build the
ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
installed package which links LAMMPS to the ScaFaCoS library.
See details on "this page"_Section_packages.html#USER-SCAFACOS.
NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
Coulombic interactions, both short- and long-range. Thus you should
NOT use a Coulmbic pair style when using kspace_style scafacos. This
also means the total Coulombic energy (short- and long-range) will be
tallied for "thermodynamic output"_thermo_style.html command as part
of the {elong} keyword; the {ecoul} keyword will be zero.
NOTE: See the current restriction below about use of ScaFaCoS in
LAMMPS with molecular charged systems or the TIP4P water model.
The specified {method} determines which ScaFaCoS algorithm is used.
These are the ScaFaCoS methods currently available from LAMMPS:
{fmm} = Fast Multi-Pole method
{p2nfft} = FFT-based Coulomb solver
{ewald} = Ewald summation
{direct} = direct O(N^2) summation
{p3m} = PPPM :ul
We plan to support additional ScaFaCoS solvers from LAMMPS in the
future. For an overview of the included solvers, refer to
"(Sutmann)"_#Sutmann2013
The specified {accuracy} is similar to the accuracy setting for other
LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
it in different ways for different methods it supports. Within the
ScaFaCoS library the {accuracy} is treated as a tolerance level
(either absolute or relative) for the chosen quantity, where the
quantity can be either the Columic field values, the per-atom Columic
energy or the total Columic energy. To select from these options, see
the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
The "kspace_modify scafacos"_kspace_modify.html command also explains
other ScaFaCoS options currently exposed to LAMMPS.
:line
The specified {accuracy} determines the relative RMS error in per-atom
forces calculated by the long-range solver. It is set as a
dimensionless number, relative to the force that two unit point
@ -321,12 +382,24 @@ dimensions. The only exception is if the slab option is set with
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
The scafacos KSpace style will only be enabled if LAMMPS is built with
the USER-SCAFACOS package. See the "Build package"_Build_package.html
doc page for more info.
The use of ScaFaCos in LAMMPS does not yet support molecular charged
systems where the short-range Coulombic interactions between atoms in
the same bond/angle/dihedral are weighted by the
"special_bonds"_special_bonds.html command. Likewise it does not
support the "TIP4P water style" where a fictitious charge site is
introduced in each water molecule.
[Related commands:]
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/long/coul/long"_pair_lj_long.html, "pair_style buck/coul/long"_pair_buck.html
lj/long/coul/long"_pair_lj_long.html, "pair_style
buck/coul/long"_pair_buck.html
[Default:]
@ -384,5 +457,12 @@ Evaluation of Forces for the Simulation of Biomolecules, University of
Illinois at Urbana-Champaign, (2006).
:link(Hardy2009)
[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009)
164-177.
[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
(2009).
:link(Sutmann2013)
[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
:link(Who2012)
[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
(2012).

11
doc/src/lammps.book
View File

@ -67,6 +67,7 @@ Howto_multiple.html
Howto_replica.html
Howto_library.html
Howto_couple.html
Howto_client_server.html
Howto_output.html
Howto_chunk.html
Howto_2d.html
@ -167,6 +168,7 @@ label.html
lattice.html
log.html
mass.html
message.html
min_modify.html
min_style.html
minimize.html
@ -194,6 +196,9 @@ reset_timestep.html
restart.html
run.html
run_style.html
server.html
server_mc.html
server_md.html
set.html
shell.html
special_bonds.html
@ -241,6 +246,7 @@ fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
fix_client_md.html
fix_cmap.html
fix_colvars.html
fix_controller.html
@ -406,6 +412,7 @@ compute_bond.html
compute_bond_local.html
compute_centro_atom.html
compute_chunk_atom.html
compute_chunk_spread_atom.html
compute_cluster_atom.html
compute_cna_atom.html
compute_cnp_atom.html
@ -461,8 +468,10 @@ compute_pressure_uef.html
compute_property_atom.html
compute_property_chunk.html
compute_property_local.html
compute_ptm_atom.html
compute_rdf.html
compute_reduce.html
compute_reduce_chunk.html
compute_rigid_local.html
compute_saed.html
compute_slice.html
@ -489,6 +498,7 @@ compute_smd_vol.html
compute_sna_atom.html
compute_spin.html
compute_stress_atom.html
compute_stress_mop.html
compute_tally.html
compute_tdpd_cc_atom.html
compute_temp.html
@ -524,6 +534,7 @@ pair_write.html
pair_adp.html
pair_agni.html
pair_airebo.html
pair_atm.html
pair_awpmd.html
pair_beck.html
pair_body_nparticle.html

162
doc/src/message.txt Normal file
View File

@ -0,0 +1,162 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Command_all.html)
:line
message command :h3
[Syntax:]
message which protocol mode arg :pre
which = {client} or {server} :ulb,l
protocol = {md} or {mc} :l
mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
{file} arg = filename
filename = file used for message exchanges
{zmq} arg = socket-ID
socket-ID for client = localhost:5555, see description below
socket-ID for server = *:5555, see description below
{mpi/one} arg = none
{mpi/two} arg = filename
filename = file used to establish communication bewteen 2 MPI jobs :pre
:ule
[Examples:]
message client md file tmp.couple
message server md file tmp.couple :pre
message client md zmq localhost:5555
message server md zmq *:5555 :pre
message client md mpi/one
message server md mpi/one :pre
message client md mpi/two tmp.couple
message server md mpi/two tmp.couple :pre
[Description:]
Establish a messaging protocol between LAMMPS and another code for the
purpose of client/server coupling.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
:line
The {which} argument defines LAMMPS to be the client or the server.
:line
The {protocol} argument defines the format and content of messages
that will be exchanged between the two codes. The current options
are:
md = run dynamics with another code
mc = perform Monte Carlo moves with another code :ul
For protocol {md}, LAMMPS can be either a client or server. See the
"server md"_server_md.html doc page for details on the protocol.
For protocol {mc}, LAMMPS can be the server. See the "server
mc"_server_mc.html doc page for details on the protocol.
:line
The {mode} argument specifies how messages are exchanged between the
client and server codes. Both codes must use the same mode and use
consistent parameters.
For mode {file}, the 2 codes communicate via binary files. They must
use the same filename, which is actually a file prefix. Several files
with that prefix will be created and deleted as a simulation runs.
The filename can include a path. Both codes must be able to access
the path/file in a common filesystem.
For mode {zmq}, the 2 codes communicate via a socket on the server
code's machine. Support for socket messaging is provided by the
open-source "ZeroMQ library"_http://zeromq.org, which must be
installed on your system. The client specifies an IP address (IPv4
format) or the DNS name of the machine the server code is running on,
followed by a 4-digit port ID for the socket, separated by a colon.
E.g.
localhost:5555 # client and server running on same machine
192.168.1.1:5555 # server is 192.168.1.1
deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre
The server specifes "*:5555" where "*" represents all available
interfaces on the server's machine, and the port ID must match
what the client specifies.
NOTE: What are allowed port IDs?
NOTE: Additional explanation is needed here about how to use the {zmq}
mode on a parallel machine, e.g. a cluster with many nodes.
For mode {mpi/one}, the 2 codes communicate via MPI and are launched
by the same mpirun command, e.g. with this syntax for OpenMPI:
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre
Note the use of the "-mpicolor color" command-line argument with
LAMMPS. See the "command-line args"_Run_options.html doc page for
further explanation.
For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
be 2 separate mpirun commands. The specified {filename} argument is a
file the 2 MPI processes will use to exchange info so that an MPI
inter-communicator can be established to enable the 2 codes to send
MPI messages to each other. Both codes must be able to access the
path/file in a common filesystem.
:line
Normally, the message command should be used at the top of a LAMMPS
input script. It performs an initial handshake with the other code to
setup messaging and to verify that both codes are using the same
message protocol and mode. Assuming both codes are launched at
(nearly) the same time, the other code should perform the same kind of
initialization.
If LAMMPS is the client code, it will begin sending messages when a
LAMMPS client command begins its operation. E.g. for the "fix
client/md"_fix_client_md.html command, it is when a "run"_run.html
command is executed.
If LAMMPS is the server code, it will begin receiving messages when
the "server"_server.html command is invoked.
A fix client command will terminate its messaging with the server when
LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
server command will terminate its messaging with the client when the
client signals it. Then the remainder of the LAMMPS input script will
be processed.
If both codes do something similar, this means a new round of
client/server messaging can be initiated after termination by re-using
a 2nd message command in your LAMMPS input script, followed by a new
fix client or server command.
:line
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"server"_server.html, "fix client/md"_fix_client_md.html
[Default:] none

13
doc/src/minimize.txt
View File

@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an
external pressure to the simulation box and allow it to shrink/expand
during the minimization.
Only a few other fixes (typically those that apply force constraints)
are invoked during minimization. See the doc pages for individual
"fix"_fix.html commands to see which ones are relevant. Current
examples of fixes that can be used include:
Only a few other fixes (typically those that add forces) are invoked
during minimization. See the doc pages for individual "fix"_fix.html
commands to see which ones are relevant. Current examples of fixes
that can be used include:
"fix addforce"_fix_addforce.html
"fix addtorque"_fix_addtorque.html
@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for
that fix. The doc pages for individual "fix"_fix.html commands
specify if this should be done.
NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc)
to be held fixed while atom coordinates are being relaxed, e.g. via
"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more
info in the Restrictions section below.
:line
[Restrictions:]

164
doc/src/pair_atm.txt Normal file
View File

@ -0,0 +1,164 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style atm command :h3
[Syntax:]
pair_style atm cutoff cutoff_triple :pre
cutoff = cutoff for each pair in 3-body interaction (distance units)
cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) :ul
[Examples:]
pair_style atm 4.5 2.5
pair_coeff * * * 0.072 :pre
pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 1 1 atm 1 0.064
pair_coeff 1 1 atm 2 0.080
pair_coeff 1 2 atm 2 0.100
pair_coeff 2 2 atm 2 0.125 :pre
[Description:]
The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod
potential for the energy E of a system of atoms as
:c,image(Eqs/pair_atm.jpg)
where nu is the three-body interaction strength. The distances
between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2,
gamma3 are as shown in this diagram:
:c,image(JPG/pair_atm_dia.jpg)
Note that for the interaction between a triplet of atoms I,J,K, there
is no "central" atom. The interaction is symmetric with respect to
permutation of the three atoms. Thus the nu value is
the same for all those permutations of the atom types of I,J,K
and needs to be specified only once, as discussed below.
The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
The potential for a triplet of atom is calculated only if all 3
distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
In addition, the product of the 3 distances r12*r23*r31 <
cutoff_triple^3 is required, which excludes from calculation the
triplets with small contribution to the interaction.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the restart files read by the
"read_restart"_read_restart.html commands:
K = atom type of the third atom (1 to Ntypes)
nu = prefactor (energy/distance^9 units) :ul
K can be specified in one of two ways. An explicit numeric value can
be used, as in the 2nd example above. J <= K is required. LAMMPS
sets the coefficients for the other 5 symmetric interactions to the
same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set
to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This
enforces the symmetry discussed above.
A wildcard asterisk can be used for K to set the coefficients for
multiple triplets of atom types. This takes the form "*" or "*n" or
"n*" or "m*n". If N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means
all types from n to N (inclusive). A middle asterisk means all types
from m to n (inclusive). Note that only type triplets with J <= K are
considered; if asterisks imply type triplets where K < J, they are
ignored.
Note that a pair_coeff command can override a previous setting for the
same I,J,K triplet. For example, these commands set nu for all I,J.K
triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet:
pair_coeff * * * 0.25
pair_coeff 2 3 4 0.1 :pre
Note that for a simulation with a single atom type, only a single
entry is required, e.g.
pair_coeff 1 1 1 0.25 :pre
For a simulation with two atom types, four pair_coeff commands will
specify all possible nu values:
pair_coeff 1 1 1 nu1
pair_coeff 1 1 2 nu2
pair_coeff 1 2 2 nu3
pair_coeff 2 2 2 nu4 :pre
For a simulation with three atom types, ten pair_coeff commands will
specify all possible nu values:
pair_coeff 1 1 1 nu1
pair_coeff 1 1 2 nu2
pair_coeff 1 1 3 nu3
pair_coeff 1 2 2 nu4
pair_coeff 1 2 3 nu5
pair_coeff 1 3 3 nu6
pair_coeff 2 2 2 nu7
pair_coeff 2 2 3 nu8
pair_coeff 2 3 3 nu9
pair_coeff 3 3 3 nu10 :pre
By default the nu value for all triplets is set to 0.0. Thus it is
not required to provide pair_coeff commands that enumerate triplet
interactions for all K types. If some I,J,K combination is not
speficied, then there will be no 3-body ATM interactions for that
combination and all its permutations. However, as with all pair
styles, it is required to specify a pair_coeff command for all I,J
combinations, else an error will result.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair styles do not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
However, if the {atm} potential is used in combination with other
potentials using the "pair_style hybrid/overlay"_pair_hybrid.html
command then pair_coeff commands need to be re-specified
in the restart input script.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Axilrod)
[(Axilrod)]
Axilrod and Teller, J Chem Phys, 11, 299 (1943);
Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).

9
doc/src/pair_coul_shield.txt
View File

@ -38,7 +38,8 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1.
Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
@ -82,5 +83,11 @@ package"_Build_package.html doc page for more info.
:line
:link(Leven3)
[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
:link(Leven4)
[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi1)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

41
doc/src/pair_ilp_graphene_hbn.txt
View File

@ -25,22 +25,24 @@ pair_coeff * * rebo CH.airebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69 :pre
[Description:]
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
potential (ILP) potential as described in "(Leven)"_#Leven and
"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
potential (ILP) potential as described in "(Leven1)"_#Leven1,
"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2.
The normals are calculated in the way as described
in "(Kolmogorov)"_#Kolmogorov2.
:c,image(Eqs/pair_ilp_graphene_hbn.jpg)
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
@ -61,13 +63,15 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
in both short- and long-range interaction regime, while the old ILP parameters
published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for
long-range interaction regime. This feature is essential for simulations in
high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance).
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide
a good description in both short- and long-range interaction regimes.
While the old ILP parameters published in "(Leven2)"_#Leven2 and
"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction
regime. This feature is essential for simulations in high pressure
regime (i.e., the interlayer distance is smaller than the equilibrium
distance). The benchmark tests and comparison of these parameters can
be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
@ -112,14 +116,17 @@ units, if your simulation does not use {metal} units.
:line
:link(Leven)
[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
:link(Leven1)
[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
:link(Leven2)
[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi2)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
:link(Kolmogorov2)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
:link(Ouyang1)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
:link(Ouyang)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

39
doc/src/pair_kolmogorov_crespi_full.txt
View File

@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
pair_coeff * * rebo CH.airebo C C
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff * * rebo CH.airebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
[Description:]
@ -38,27 +38,32 @@ forces and to include all the pairs to build the neighbor list for
calculating the normals. Energies are shifted so that they go
continuously to zero at the cutoff assuming that the exponential part of
{Vij} (first term) decays sufficiently fast. This shift is achieved by
the last term in the equation for {Vij} above.
the last term in the equation for {Vij} above. This is essential only
when the tapper function is turned off. The formula of taper function
can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential is intended for interactions between two different
graphene layers. Therefore, to avoid interaction within the same layers,
each layer should have a separate molecule id and is recommended to use
"full" atom style in the data file.
The parameter file (e.g. CC.KC), is intended for use with {metal}
The parameter file (e.g. CH.KC), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters, {S},
and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC)
is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
a good description in both short- and long-range interaction regime,
while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1
are only suitable for long-range interaction regime.
This feature is essential for simulations in high-pressure regime
(i.e., the interlayer distance smaller than the equilibrium distance).
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC
(without the taper function) and CH_taper.KC (with the taper function)
are presented in "(Ouyang)"_#Ouyang1. The energy for the KC potential
with the taper function goes continuously to zero at the cutoff. The
parameters in both CH.KC and CH_taper.KC provide a good description in
both short- and long-range interaction regimes. While the original
parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only
suitable for long-range interaction regime. This feature is essential
for simulations in high pressure regime (i.e., the interlayer distance
is smaller than the equilibrium distance). The benchmark tests and
comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
@ -84,7 +89,7 @@ package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
The CC.KC potential file provided with LAMMPS (see the potentials
The CH.KC potential file provided with LAMMPS (see the potentials
folder) are parameterized for metal units. You can use this potential
with any LAMMPS units, but you would need to create your own custom
CC.KC potential file with all coefficients converted to the appropriate
@ -105,5 +110,5 @@ units.
:link(Kolmogorov1)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
:link(Ouyang2)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
:link(Ouyang1)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

1
doc/src/pair_style.txt
View File

@ -103,6 +103,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor

1
doc/src/pairs.txt
View File

@ -8,6 +8,7 @@ Pair Styles :h1
pair_adp
pair_agni
pair_airebo
pair_atm
pair_awpmd
pair_beck
pair_body_nparticle

71
doc/src/server.txt Normal file
View File

@ -0,0 +1,71 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
server command :h3
[Syntax:]
server protocol :pre
protocol = {md} or {mc} :ul
[Examples:]
server md :pre
[Description:]
This command starts LAMMPS running in "server" mode, where it receives
messages from a separate "client" code and responds by sending a reply
message back to the client. The specified {protocol} determines the
format and content of messages LAMMPS expects to receive and how it
responds.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
signals when it is done sending messages to LAMMPS, at which point the
loop will exit, and the remainder of the LAMMPS script will be
processed.
The {protocol} argument defines the format and content of messages
that will be exchanged between the two codes. The current options
are:
"md"_server_md.html = run dynamics with another code
"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
For protocol {md}, LAMMPS can be either a client (via the "fix
client/md"_fix_client_md.html command) or server. See the "server
md"_server_md.html doc page for details on the protocol.
For protocol {mc}, LAMMPS can be the server. See the "server
mc"_server_mc.html doc page for details on the protocol.
:line
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
the other client code.
[Related commands:]
"message"_message.html, "fix client/md"_fix_client_md.html
[Default:] none

116
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@ -0,0 +1,116 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
server mc command :h3
[Syntax:]
server mc :pre
mc = the protocol argument to the "server"_server.html command
[Examples:]
server mc :pre
[Description:]
This command starts LAMMPS running in "server" mode, where it will
expect messages from a separate "client" code that match the {mc}
protocol for format and content explained below. For each message
LAMMPS receives it will send a message back to the client.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
signals when it is done sending messages to LAMMPS, at which point the
loop will exit, and the remainder of the LAMMPS script will be
processed.
The "server"_server.html doc page gives other options for using LAMMPS
See an example of how this command is used in
examples/COUPLE/lammps_mc/in.server.
:line
When using this command, LAMMPS (as the server code) receives
instructions from a Monte Carlo (MC) driver to displace random atoms,
compute the energy before and after displacement, and run dynamics to
equilibrate the system.
The MC driver performs the random displacements on random atoms,
accepts or rejects the move in an MC sense, and orchestrates the MD
runs.
The format and content of the exchanged messages are explained here in
a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
pages for more details on the actual library syntax. The "cs" object
in this pseudo code is a pointer to an instance of the CSlib.
See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
example of how an MC driver code can use these messages.
Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
[Client sends one of these kinds of message]:
cs->send(NATOMS,0) # msgID = 1 with no fields :pre
cs->send(EINIT,0) # msgID = 2 with no fields :pre
cs->send(DISPLACE,2) # msgID = 3 with 2 fields
cs->pack_int(1,ID) # 1st field = ID of atom to displace
cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
cs->send(ACCEPT,1) # msgID = 4 with 1 field
cs->pack_int(1,flag) # 1st field = accept/reject flag :pre
cs->send(RUN,1) # msgID = 5 with 1 field
cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
[Server replies]:
cs->send(NATOMS,1) # msgID = 1 with 1 field
cs->pack_int(1,natoms) # 1st field = number of atoms :pre
cs->send(EINIT,2) # msgID = 2 with 2 fields
cs->pack_double(1,poteng) # 1st field = potential energy of system
cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
cs->send(DISPLACE,1) # msgID = 3 with 1 field
cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
cs->send(ACCEPT,0) # msgID = 4 with no fields :pre
cs->send(RUN,0) # msgID = 5 with no fields :pre
:line
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
the other client code.
[Related commands:]
"message"_message.html
[Default:] none

149
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@ -0,0 +1,149 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
server md command :h3
[Syntax:]
server md :pre
md = the protocol argument to the "server"_server.html command
[Examples:]
server md :pre
[Description:]
This command starts LAMMPS running in "server" mode, where it will
expect messages from a separate "client" code that match the {md}
protocol for format and content explained below. For each message
LAMMPS receives it will send a message back to the client.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
signals when it is done sending messages to LAMMPS, at which point the
loop will exit, and the remainder of the LAMMPS script will be
processed.
The "server"_server.html doc page gives other options for using LAMMPS
in server mode. See an example of how this command is used in
examples/message/in.message.server.
:line
When using this command, LAMMPS (as the server code) receives the
current coordinates of all particles from the client code each
timestep, computes their interaction, and returns the energy, forces,
and pressure for the interacting particles to the client code, so it
can complete the timestep. This command could also be used with a
client code that performs energy minimization, using the server to
compute forces and energy each iteration of its minimizer.
When using the "fix client/md"_fix_client_md.html command, LAMMPS (as
the client code) does the timestepping and receives needed energy,
forces, and pressure values from the server code.
The format and content of the exchanged messages are explained here in
a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
pages for more details on the actual library syntax. The "cs" object
in this pseudo code is a pointer to an instance of the CSlib.
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
files for details on how LAMMPS uses these messages. See the
examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
a quantum code (VASP) can use use these messages.
The following pseudo-code uses these values, defined as enums.
Define:
SETUP=1, STEP=2
DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10
FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre
[Client sends 2 kinds of messages]:
# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
# optional fields: UNITS, CHARGE :pre
cs->send(SETUP,nfields) # msgID with nfields :pre
cs->pack_int(DIM,dim) # dimension (2,3) of simulation
cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
cs->pack(BOX,9,box) # 3 edge vectors of simulation box
cs->pack_int(NATOMS,natoms) # total number of atoms
cs->pack_int(NTYPES,ntypes) # number of atom types
cs->pack(TYPES,natoms,type) # vector of per-atom types
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
# required fields: COORDS
# optional fields: ORIGIN, BOX :pre
cs->send(STEP,nfields) # msgID with nfields :pre
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre
[Server replies to either kind of message]:
# required fields: FORCES, ENERGY, PRESSURE
# optional fields: ERROR :pre
cs->send(msgID,nfields) # msgID with nfields
cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
cs->pack(ENERGY,1,poteng) # total potential energy of system
cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre
:line
The units for various quantities that are sent and received iva
messages are defined for atomic-scale simulations in the table below.
The client and server codes (including LAMMPS) can use internal units
different than these (e.g. "real units"_units.html in LAMMPS), so long
as they convert to these units for meesaging.
COORDS, ORIGIN, BOX = Angstroms
CHARGE = multiple of electron charge (1.0 is a proton)
ENERGY = eV
FORCES = eV/Angstrom
PRESSURE = bars :ul
Note that these are "metal units"_units.html in LAMMPS.
If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
units"_units.html, then the client and server should exchange a UNITS
message as indicated above, and both the client and server should
agree on the units for the data they exchange.
:line
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"message"_message.html, "fix client/md"_fix_client_md.html
[Default:] none

5
examples/COUPLE/README
View File

@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
In all of the examples included here, LAMMPS must first be built as a
library. Basically, in the src dir you type one of
@ -33,9 +34,13 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
lammps_mc client/server coupling of Monte Carlo client
with LAMMPS server for energy evaluation
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
lammps_vasp client/server coupling of LAMMPS client with
VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran

33
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# Makefile for MC
SHELL = /bin/sh
SRC = mc.cpp random_park.cpp
OBJ = $(SRC:.cpp=.o)
# change this line for your machine to path for CSlib src dir
CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
# compiler/linker settings
CC = g++
CCFLAGS = -g -O3 -I$(CSLIB)
LINK = g++
LINKFLAGS = -g -O -L$(CSLIB)
# targets
mc: $(OBJ)
# first line if built the CSlib within lib/message with ZMQ support
# second line if built the CSlib without ZMQ support
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
clean:
@rm -f *.o mc
# rules
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<

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Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE)
and Section_howto.html#howto10 for more details on how
client/server coupling works in LAMMPS.
In this dir, the mc.cpp/h files are a standalone "client" MC code. It
should be run on a single processor, though it could become a parallel
program at some point. LAMMPS is also run as a standalone executable
as a "server" on as many processors as desired using its "server mc"
command; see it's doc page for details.
Messages are exchanged between MC and LAMMPS via a client/server
library (CSlib), which is included in the LAMMPS distribution in
lib/message. As explained below you can choose to exchange data
between the two programs either via files or sockets (ZMQ). If the MC
program became parallel, data could also be exchanged via MPI.
The MC code makes simple MC moves, by displacing a single random atom
by a small random amount. It uses LAMMPS to calculate the energy
change, and to run dynamics between MC moves.
----------------
Build LAMMPS with its MESSAGE package installed:
See the Build extras doc page and its MESSAGE package
section for details.
CMake:
-D PKG_MESSAGE=yes # include the MESSAGE package
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
Traditional make:
% cd lammps/lib/message
% python Install.py -m -z # build CSlib with MPI and ZMQ support
% cd lammps/src
% make yes-message
% make mpi
You can leave off the -z if you do not have ZMQ on your system.
----------------
Build the MC client code
The source files for the MC code are in this dir. It links with the
CSlib library in lib/message/cslib.
You must first build the CSlib in serial mode, e.g.
% cd lammps/lib/message/cslib/src
% make lib # build serial and parallel lib with ZMQ support
% make lib zmq=no # build serial and parallel lib without ZMQ support
Then edit the Makefile in this dir. The CSLIB variable should be the
path to where the LAMMPS lib/message/cslib/src dir is on your system.
If you built the CSlib without ZMQ support you will also need to
comment/uncomment one line. Then you can just type
% make
and you should get an "mc" executable.
----------------
To run in client/server mode:
Both the client (MC) and server (LAMMPS) must use the same messaging
mode, namely file or zmq. This is an argument to the MC code; it can
be selected by setting the "mode" variable when you run LAMMPS. The
default mode = file.
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
package was installed with socket (ZMQ) support. This means either of
the messaging modes can be used and LAMMPS can be run in serial or
parallel. The MC code is always run in serial.
When you run, the server should print out thermodynamic info
for every MD run it performs (between MC moves). The client
will print nothing until the simulation ends, then it will
print stats about the accepted MC moves.
The examples below are commands you should use in two different
terminal windows. The order of the two commands (client or server
launch) does not matter. You can run them both in the same window if
you append a "&" character to the first one to run it in the
background.
--------------
File mode of messaging:
% mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
% mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
ZMQ mode of messaging:
% mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
% mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
--------------
The input script for the MC program is in.mc. You can edit it to run
longer simulations.
500 nsteps = total # of steps of MD
100 ndynamics = # of MD steps between MC moves
0.1 delta = displacement size of MC move
1.0 temperature = used in MC Boltzman factor
12345 seed = random number seed
--------------
The problem size that LAMMPS is computing the MC energy for and
running dynamics on is set by the x,y,z variables in the LAMMPS
in.mc.server script. The default size is 500 particles. You can
adjust the size as follows:
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles

7
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@ -0,0 +1,7 @@
# MC params
500 nsteps
100 ndynamics
0.1 delta
1.0 temperature
12345 seed

36
examples/COUPLE/lammps_mc/in.mc.server Normal file
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@ -0,0 +1,36 @@
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then &
"message server mc file tmp.couple" &
elif "${mode} == zmq" &
"message server mc zmq *:5555" &
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc

254
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@ -0,0 +1,254 @@
LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc file tmp.couple
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000649929 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
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) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
93.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19500 ave 19500 max 19500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
93.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19501 ave 19501 max 19501 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
157.3% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1939 ave 1939 max 1939 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18757 ave 18757 max 18757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18757
Ave neighs/atom = 37.514
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
139.8% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18699 ave 18699 max 18699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
139.8% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18715 ave 18715 max 18715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18715
Ave neighs/atom = 37.43
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
157.3% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18683 ave 18683 max 18683 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18683
Ave neighs/atom = 37.366
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
Total wall time: 0:00:02

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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc file tmp.couple
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000592947 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
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) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
59.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.815e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875 ave 4875 max 4875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
106.9% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875.25 ave 4885 max 4866 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
113.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.755e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1085.25 ave 1089 max 1079 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 4690.25 ave 4996 max 4401 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 18761
Ave neighs/atom = 37.522
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
117.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.563e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 1068.5 ave 1076 max 1063 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4674.75 ave 4938 max 4419 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
93.9% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.994e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1069 ave 1080 max 1055 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4672 ave 4803 max 4600 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 18688
Ave neighs/atom = 37.376
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
111.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.576e-06 | | |100.00
Nlocal: 125 ave 132 max 118 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1057.5 ave 1068 max 1049 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 4685.75 ave 5045 max 4229 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 18743
Ave neighs/atom = 37.486
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
Total wall time: 0:00:02

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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc zmq *:5555
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000741005 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
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) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
52.4% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19500 ave 19500 max 19500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
52.4% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19501 ave 19501 max 19501 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
83.9% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1939 ave 1939 max 1939 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18757 ave 18757 max 18757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18757
Ave neighs/atom = 37.514
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
209.7% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18699 ave 18699 max 18699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
104.9% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18715 ave 18715 max 18715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18715
Ave neighs/atom = 37.43
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
209.7% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18683 ave 18683 max 18683 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18683
Ave neighs/atom = 37.366
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
Total wall time: 0:00:00

254
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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc zmq *:5555
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000576019 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
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) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
89.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.768e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875 ave 4875 max 4875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
94.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.457e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875.25 ave 4885 max 4866 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
115.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1085.25 ave 1089 max 1079 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 4690.25 ave 4996 max 4401 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 18761
Ave neighs/atom = 37.522
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
125.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.384e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 1068.5 ave 1076 max 1063 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4674.75 ave 4938 max 4419 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
112.5% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.444e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1069 ave 1080 max 1055 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4672 ave 4803 max 4600 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 18688
Ave neighs/atom = 37.376
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
139.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 125 ave 132 max 118 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1057.5 ave 1068 max 1049 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 4685.75 ave 5045 max 4229 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 18743
Ave neighs/atom = 37.486
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
Total wall time: 0:00:00

263
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */
// MC code used with LAMMPS in client/server mode
// MC is the client, LAMMPS is the server
// Syntax: mc infile mode modearg
// mode = file, zmq
// modearg = filename for file, localhost:5555 for zmq
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "mc.h"
#include "random_park.h"
#include "cslib.h"
using namespace CSLIB_NS;
void error(const char *);
CSlib *cs_create(char *, char *);
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
// main program
int main(int narg, char **arg)
{
if (narg != 4) {
error("Syntax: mc infile mode modearg");
exit(1);
}
// initialize CSlib
CSlib *cs = cs_create(arg[2],arg[3]);
// create MC class and perform run
MC *mc = new MC(arg[1],cs);
mc->run();
// final MC stats
int naccept = mc->naccept;
int nattempt = mc->nattempt;
printf("------ MC stats ------\n");
printf("MC attempts = %d\n",nattempt);
printf("MC accepts = %d\n",naccept);
printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
// clean up
delete cs;
delete mc;
}
/* ---------------------------------------------------------------------- */
void error(const char *str)
{
printf("ERROR: %s\n",str);
exit(1);
}
/* ---------------------------------------------------------------------- */
CSlib *cs_create(char *mode, char *arg)
{
CSlib *cs = new CSlib(0,mode,arg,NULL);
// initial handshake to agree on protocol
cs->send(0,1);
cs->pack_string(1,(char *) "mc");
int msgID,nfield;
int *fieldID,*fieldtype,*fieldlen;
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
return cs;
}
// ----------------------------------------------------------------------
// MC class
// ----------------------------------------------------------------------
MC::MC(char *mcfile, void *cs_caller)
//MC::MC(char *mcfile, CSlib *cs_caller)
{
cs_void = cs_caller;
// setup MC params
options(mcfile);
// random # generator
random = new RanPark(seed);
}
/* ---------------------------------------------------------------------- */
MC::~MC()
{
free(x);
delete random;
}
/* ---------------------------------------------------------------------- */
void MC::run()
{
int iatom,accept,msgID,nfield;
double pe_initial,pe_final,edelta;
double dx,dy,dz;
double xold[3],xnew[3];
int *fieldID,*fieldtype,*fieldlen;
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
CSlib *cs = (CSlib *) cs_void;
// one-time request for atom count from MD
// allocate 1d coord buffer
cs->send(NATOMS,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
natoms = cs->unpack_int(1);
x = (double *) malloc(3*natoms*sizeof(double));
// loop over MC moves
naccept = nattempt = 0;
for (int iloop = 0; iloop < nloop; iloop++) {
// request current energy from MD
// recv energy, coords from MD
cs->send(EINIT,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
pe_initial = cs->unpack_double(1);
double *x = (double *) cs->unpack(2);
// perform simple MC event
// displace a single atom by random amount
iatom = (int) natoms*random->uniform();
xold[0] = x[3*iatom+0];
xold[1] = x[3*iatom+1];
xold[2] = x[3*iatom+2];
dx = 2.0*delta*random->uniform() - delta;
dy = 2.0*delta*random->uniform() - delta;
dz = 2.0*delta*random->uniform() - delta;
xnew[0] = xold[0] + dx;
xnew[1] = xold[1] + dx;
xnew[2] = xold[2] + dx;
// send atom ID and its new coords to MD
// recv new energy
cs->send(DISPLACE,2);
cs->pack_int(1,iatom+1);
cs->pack(2,4,3,xnew);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
pe_final = cs->unpack_double(1);
// decide whether to accept/reject MC event
if (pe_final <= pe_initial) accept = 1;
else if (temperature == 0.0) accept = 0;
else if (random->uniform() >
exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
else accept = 1;
nattempt++;
if (accept) naccept++;
// send accept (1) or reject (0) flag to MD
cs->send(ACCEPT,1);
cs->pack_int(1,accept);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
// send dynamics timesteps
cs->send(RUN,1);
cs->pack_int(1,ndynamics);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
}
// send exit message to MD
cs->send(-1,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
}
/* ---------------------------------------------------------------------- */
void MC::options(char *filename)
{
// default params
nsteps = 0;
ndynamics = 100;
delta = 0.1;
temperature = 1.0;
seed = 12345;
// read and parse file
FILE *fp = fopen(filename,"r");
if (fp == NULL) error("Could not open MC file");
char line[MAXLINE];
char *keyword,*value;
char *eof = fgets(line,MAXLINE,fp);
while (eof) {
if (line[0] == '#') { // comment line
eof = fgets(line,MAXLINE,fp);
continue;
}
value = strtok(line," \t\n\r\f");
if (value == NULL) { // blank line
eof = fgets(line,MAXLINE,fp);
continue;
}
keyword = strtok(NULL," \t\n\r\f");
if (keyword == NULL) error("Missing keyword in MC file");
if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
else if (strcmp(keyword,"delta") == 0) delta = atof(value);
else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
else error("Unknown param in MC file");
eof = fgets(line,MAXLINE,fp);
}
// derived params
nloop = nsteps/ndynamics;
}

40
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */
#ifndef MC_H
#define MC_H
/* ---------------------------------------------------------------------- */
class MC {
public:
int naccept; // # of accepted MC events
int nattempt; // # of attempted MC events
MC(char *, void *);
~MC();
void run();
private:
int nsteps; // total # of MD steps
int ndynamics; // steps in one short dynamics run
int nloop; // nsteps/ndynamics
int natoms; // # of MD atoms
double delta; // MC displacement distance
double temperature; // MC temperature for Boltzmann criterion
double *x; // atom coords as 3N 1d vector
double energy; // global potential energy
int seed; // RNG seed
class RanPark *random;
void *cs_void; // messaging library
void options(char *);
};
#endif

72
examples/COUPLE/lammps_mc/random_park.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// Park/Miller RNG
#include <math.h>
#include "random_park.h"
//#include "error.h"
#define IA 16807
#define IM 2147483647
#define AM (1.0/IM)
#define IQ 127773
#define IR 2836
/* ---------------------------------------------------------------------- */
RanPark::RanPark(int seed_init)
{
//if (seed_init <= 0)
// error->one(FLERR,"Invalid seed for Park random # generator");
seed = seed_init;
save = 0;
}
/* ----------------------------------------------------------------------
uniform RN
------------------------------------------------------------------------- */
double RanPark::uniform()
{
int k = seed/IQ;
seed = IA*(seed-k*IQ) - IR*k;
if (seed < 0) seed += IM;
double ans = AM*seed;
return ans;
}
/* ----------------------------------------------------------------------
gaussian RN
------------------------------------------------------------------------- */
double RanPark::gaussian()
{
double first,v1,v2,rsq,fac;
if (!save) {
do {
v1 = 2.0*uniform()-1.0;
v2 = 2.0*uniform()-1.0;
rsq = v1*v1 + v2*v2;
} while ((rsq >= 1.0) || (rsq == 0.0));
fac = sqrt(-2.0*log(rsq)/rsq);
second = v1*fac;
first = v2*fac;
save = 1;
} else {
first = second;
save = 0;
}
return first;
}

28
examples/COUPLE/lammps_mc/random_park.h Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef RANPARK_H
#define RANPARK_H
class RanPark {
public:
RanPark(int);
double uniform();
double gaussian();
private:
int seed,save;
double second;
};
#endif

53
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# Startparameter for this run:
NWRITE = 2 write-flag & timer
PREC = normal normal or accurate (medium, high low for compatibility)
ISTART = 0 job : 0-new 1-cont 2-samecut
ICHARG = 2 charge: 1-file 2-atom 10-const
ISPIN = 1 spin polarized calculation?
LSORBIT = F spin-orbit coupling
INIWAV = 1 electr: 0-lowe 1-rand 2-diag
# Electronic Relaxation 1
ENCUT = 600.0 eV #Plane wave energy cutoff
ENINI = 600.0 initial cutoff
NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
EDIFF = 0.1E-05 stopping-criterion for ELM
# Ionic relaxation
EDIFFG = 0.1E-02 stopping-criterion for IOM
NSW = 0 number of steps for IOM
NBLOCK = 1; KBLOCK = 1 inner block; outer block
IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
NFREE = 0 steps in history (QN), initial steepest desc. (CG)
ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
POTIM = 0.5000 time-step for ionic-motion
TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
SMASS = -3.00 Nose mass-parameter (am)
estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
PSTRESS= 0.0 pullay stress
# DOS related values:
EMIN = 10.00; EMAX =-10.00 energy-range for DOS
EFERMI = 0.00
ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
# Electronic relaxation 2 (details)
IALGO = 48 algorithm
# Write flags
LWAVE = T write WAVECAR
LCHARG = T write CHGCAR
LVTOT = F write LOCPOT, total local potential
LVHAR = F write LOCPOT, Hartree potential only
LELF = F write electronic localiz. function (ELF)
# Dipole corrections
LMONO = F monopole corrections only (constant potential shift)
LDIPOL = F correct potential (dipole corrections)
IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
EPSILON= 1.0000000 bulk dielectric constant
# Exchange correlation treatment:
GGA = -- GGA type

6
examples/COUPLE/lammps_vasp/KPOINTS Normal file
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K-Points
0
Monkhorst Pack
15 15 15
0 0 0

11
examples/COUPLE/lammps_vasp/POSCAR_W Normal file
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W unit cell
1.0
3.16 0.00000000 0.00000000
0.00000000 3.16 0.00000000
0.00000000 0.00000000 3.16
W
2
Direct
0.00000000 0.00000000 0.00000000
0.50000000 0.50000000 0.50000000

149
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Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
Section_howto.html#howto10 for more details on how client/server
coupling works in LAMMPS.
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
code so it can work as a "server" code which LAMMPS drives as a
"client" code to perform ab initio MD. LAMMPS performs the MD
timestepping, sends VASP a current set of coordinates each timestep,
VASP computes forces and energy and virial and returns that info to
LAMMPS.
Messages are exchanged between MC and LAMMPS via a client/server
library (CSlib), which is included in the LAMMPS distribution in
lib/message. As explained below you can choose to exchange data
between the two programs either via files or sockets (ZMQ). If the
vasp_wrap.py program became parallel, or the CSlib library calls were
integrated into VASP directly, then data could also be exchanged via
MPI.
----------------
Build LAMMPS with its MESSAGE package installed:
See the Build extras doc page and its MESSAGE package
section for details.
CMake:
-D PKG_MESSAGE=yes # include the MESSAGE package
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
Traditional make:
cd lammps/lib/message
python Install.py -m -z # build CSlib with MPI and ZMQ support
cd lammps/src
make yes-message
make mpi
You can leave off the -z if you do not have ZMQ on your system.
----------------
Build the CSlib in a form usable by the vasp_wrapper.py script:
% cd lammps/lib/message/cslib/src
% make shlib # build serial and parallel shared lib with ZMQ support
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
This will make a shared library versions of the CSlib, which Python
requires. Python must be able to find both the cslib.py script and
the libcsnompi.so library in your lammps/lib/message/cslib/src
directory. If it is not able to do this, you will get an error when
you run vasp_wrapper.py.
You can do this by augmenting two environment variables, either
from the command line, or in your shell start-up script.
Here is the sample syntax for the csh or tcsh shells:
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
----------------
Prepare to use VASP and the vasp_wrapper.py script
You can run the vasp_wrap.py script as-is to test that the coupling
between it and LAMMPS is functional. This will use the included
vasprun.xml file output by a previous VASP run.
But note that the as-is version of vasp_wrap.py will not attempt to
run VASP.
To do this, you must edit the 1st vaspcmd line at the top of
vasp_wrapper.py to be the launch command needed to run VASP on your
system. It can be a command to run VASP in serial or in parallel,
e.g. an mpirun command. Then comment out the 2nd vaspcmd line
immediately following it.
Insure you have the necessary VASP input files in this
directory, suitable for the VASP calculation you want to perform:
INCAR
KPOINTS
POSCAR_template
POTCAR
Examples of all but the POTCAR file are provided. As explained below,
POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
be used to test the LAMMPS/VASP coupling. The POTCAR file is a
proprietary VASP file, so use one from your VASP installation.
Note that the POSCAR_template file should be matched to the LAMMPS
input script (# of atoms and atom types, box size, etc). The provided
POSCAR_W matches in.client.W.
Once you run VASP yourself, the vasprun.xml file will be overwritten.
----------------
To run in client/server mode:
NOTE: The vasp_wrap.py script must be run with Python version 2, not
3. This is because it used the CSlib python wrapper, which only
supports version 2. We plan to upgrade CSlib to support Python 3.
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
messaging mode, namely file or zmq. This is an argument to the
vasp_wrap.py code; it can be selected by setting the "mode" variable
when you run LAMMPS. The default mode = file.
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
package was installed with socket (ZMQ) support. This means either of
the messaging modes can be used and LAMMPS can be run in serial or
parallel. The vasp_wrap.py code is always run in serial, but it
launches VASP from Python via an mpirun command which can run VASP
itself in parallel.
When you run, the server should print out thermodynamic info every
timestep which corresponds to the forces and virial computed by VASP.
VASP will also generate output files each timestep. The vasp_wrapper.py
script could be generalized to archive these.
The examples below are commands you should use in two different
terminal windows. The order of the two commands (client or server
launch) does not matter. You can run them both in the same window if
you append a "&" character to the first one to run it in the
background.
--------------
File mode of messaging:
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
% python vasp_wrap.py file POSCAR_W
% mpirun -np 2 lmp_mpi -v mode file < in.client.W
% python vasp_wrap.py file POSCAR_W
ZMQ mode of messaging:
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
% python vasp_wrap.py zmq POSCAR_W
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
% python vasp_wrap.py zmq POSCAR_W

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@ -0,0 +1,15 @@
LAMMPS W data file
2 atoms
1 atom types
0.0 3.16 xlo xhi
0.0 3.16 ylo yhi
0.0 3.16 zlo zhi
Atoms
1 1 0.000 0.000 0.000
2 1 1.58 1.58 1.58

34
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@ -0,0 +1,34 @@
# small W unit cell for use with VASP
variable mode index file
if "${mode} == file" then &
"message client md file tmp.couple" &
elif "${mode} == zmq" &
"message client md zmq localhost:5555" &
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
mass 1 183.85
replicate $x $y $z
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3

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@ -0,0 +1,76 @@
LAMMPS (22 Aug 2018)
# small W unit cell for use with VASP
variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md zmq localhost:5555
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 2 MPI processor grid
reading atoms ...
2 atoms
mass 1 183.85
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 2 MPI processor grid
2 atoms
Time spent = 0.000148058 secs
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 -48.030793 -78159.503
1 298.24318 0 0 -48.03102 -78167.19
2 296.85584 0 0 -48.031199 -78173.26
3 295.83795 0 0 -48.031331 -78177.714
Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
50.1% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
Other | | 1.204e-05 | | | 0.00
Nlocal: 1 ave 1 max 1 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 4 ave 4 max 4 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:01:21

300
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#!/usr/bin/env python
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------
# Syntax: vasp_wrap.py file/zmq POSCARfile
# wrapper on VASP to act as server program using CSlib
# receives message with list of coords from client
# creates VASP inputs
# invokes VASP to calculate self-consistent energy of that config
# reads VASP outputs
# sends message with energy, forces, pressure to client
# NOTES:
# check to insure basic VASP input files are in place?
# could archive VASP input/output in special filenames or dirs?
# need to check that POTCAR file is consistent with atom ordering?
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
from __future__ import print_function
import sys
version = sys.version_info[0]
if version == 3:
sys.exit("The CSlib python wrapper does not yet support python 3")
import subprocess
import xml.etree.ElementTree as ET
from cslib import CSlib
# comment out 2nd line once 1st line is correct for your system
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
vaspcmd = "touch tmp"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
# -------------------------------------
# functions
# error message and exit
def error(txt):
print("ERROR:",txt)
sys.exit(1)
# -------------------------------------
# read initial VASP POSCAR file to setup problem
# return natoms,ntypes,box
def vasp_setup(poscar):
ps = open(poscar,'r').readlines()
# box size
words = ps[2].split()
xbox = float(words[0])
words = ps[3].split()
ybox = float(words[1])
words = ps[4].split()
zbox = float(words[2])
box = [xbox,ybox,zbox]
ntypes = 0
natoms = 0
words = ps[6].split()
for word in words:
if word == '#': break
ntypes += 1
natoms += int(word)
return natoms,ntypes,box
# -------------------------------------
# write a new POSCAR file for VASP
def poscar_write(poscar,natoms,ntypes,types,coords,box):
psold = open(poscar,'r').readlines()
psnew = open("POSCAR",'w')
# header, including box size
psnew.write(psold[0])
psnew.write(psold[1])
psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
psnew.write(psold[5])
psnew.write(psold[6])
# per-atom coords
# grouped by types
psnew.write("Cartesian\n")
for itype in range(1,ntypes+1):
for i in range(natoms):
if types[i] != itype: continue
x = coords[3*i+0]
y = coords[3*i+1]
z = coords[3*i+2]
aline = " %g %g %g\n" % (x,y,z)
psnew.write(aline)
psnew.close()
# -------------------------------------
# read a VASP output vasprun.xml file
# uses ElementTree module
# see https://docs.python.org/2/library/xml.etree.elementtree.html
def vasprun_read():
tree = ET.parse('vasprun.xml')
root = tree.getroot()
#fp = open("vasprun.xml","r")
#root = ET.parse(fp)
scsteps = root.findall('calculation/scstep')
energy = scsteps[-1].find('energy')
for child in energy:
if child.attrib["name"] == "e_0_energy":
eout = float(child.text)
fout = []
sout = []
varrays = root.findall('calculation/varray')
for varray in varrays:
if varray.attrib["name"] == "forces":
forces = varray.findall("v")
for line in forces:
fxyz = line.text.split()
fxyz = [float(value) for value in fxyz]
fout += fxyz
if varray.attrib["name"] == "stress":
tensor = varray.findall("v")
stensor = []
for line in tensor:
sxyz = line.text.split()
sxyz = [float(value) for value in sxyz]
stensor.append(sxyz)
sxx = stensor[0][0]
syy = stensor[1][1]
szz = stensor[2][2]
# symmetrize off-diagonal components
sxy = 0.5 * (stensor[0][1] + stensor[1][0])
sxz = 0.5 * (stensor[0][2] + stensor[2][0])
syz = 0.5 * (stensor[1][2] + stensor[2][1])
sout = [sxx,syy,szz,sxy,sxz,syz]
#fp.close()
return eout,fout,sout
# -------------------------------------
# main program
# command-line args
if len(sys.argv) != 3:
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
mode = sys.argv[1]
poscar_template = sys.argv[2]
if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
else:
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
natoms,ntypes,box = vasp_setup(poscar_template)
# initial message for MD protocol
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID != 0: error("Bad initial client/server handshake")
protocol = cs.unpack_string(1)
if protocol != "md": error("Mismatch in client/server protocol")
cs.send(0,0)
# endless server loop
while 1:
# recv message from client
# msgID = 0 = all-done message
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID < 0: break
# SETUP receive at beginning of each run
# required fields: DIM, PERIODICTY, ORIGIN, BOX,
# NATOMS, NTYPES, TYPES, COORDS
# optional fields: others in enum above, but VASP ignores them
if msgID == SETUP:
origin = []
box = []
natoms_recv = ntypes_recv = 0
types = []
coords = []
for field in fieldID:
if field == DIM:
dim = cs.unpack_int(DIM)
if dim != 3: error("VASP only performs 3d simulations")
elif field == PERIODICITY:
periodicity = cs.unpack(PERIODICITY,1)
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
error("VASP wrapper only currently supports fully periodic systems")
elif field == ORIGIN:
origin = cs.unpack(ORIGIN,1)
elif field == BOX:
box = cs.unpack(BOX,1)
elif field == NATOMS:
natoms_recv = cs.unpack_int(NATOMS)
if natoms != natoms_recv:
error("VASP wrapper mis-match in number of atoms")
elif field == NTYPES:
ntypes_recv = cs.unpack_int(NTYPES)
if ntypes != ntypes_recv:
error("VASP wrapper mis-match in number of atom types")
elif field == TYPES:
types = cs.unpack(TYPES,1)
elif field == COORDS:
coords = cs.unpack(COORDS,1)
if not origin or not box or not natoms or not ntypes or \
not types or not coords:
error("Required VASP wrapper setup field not received");
# STEP receive at each timestep of run or minimization
# required fields: COORDS
# optional fields: ORIGIN, BOX
elif msgID == STEP:
coords = []
for field in fieldID:
if field == COORDS:
coords = cs.unpack(COORDS,1)
elif field == ORIGIN:
origin = cs.unpack(ORIGIN,1)
elif field == BOX:
box = cs.unpack(BOX,1)
if not coords: error("Required VASP wrapper step field not received");
else: error("VASP wrapper received unrecognized message")
# create POSCAR file
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
# invoke VASP
print("\nLaunching VASP ...")
print(vaspcmd)
subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
# process VASP output
energy,forces,virial = vasprun_read()
# convert VASP kilobars to bars
for i,value in enumerate(virial): virial[i] *= 1000.0
# return forces, energy, pressure to client
cs.send(msgID,3);
cs.pack(FORCES,4,3*natoms,forces)
cs.pack_double(ENERGY,energy)
cs.pack(VIRIAL,4,6,virial)
# final reply to client
cs.send(0,0)
# clean-up
del cs

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2
examples/README
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@ -59,6 +59,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
airebo: polyethylene with AIREBO potential
atm: Axilrod-Teller-Muto potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
@ -82,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model

5
examples/USER/diffraction/BulkNi.in
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@ -17,8 +17,9 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd

35
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@ -1,35 +0,0 @@
variable A string bulkNi
log $A.log
boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
dump 1 all custom 1 $A.dump id x y z
run 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED

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@ -0,0 +1,40 @@
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 1000
thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0

111
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@ -0,0 +1,111 @@
LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 1 by 1 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
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 = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms
167.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 1224 ave 1224 max 1224 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2975 ave 2975 max 2975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40241 ave 40241 max 40241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 2 by 2 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
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 = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms
65.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.065e-05 | | |100.00
Nlocal: 306 ave 320 max 295 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1450.25 ave 1485 max 1422 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 10060.2 ave 10866 max 9507 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

185
examples/USER/misc/mop/moppz.time.reference Normal file
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# Time-averaged data for fix moppzt
# TimeStep Number-of-rows
# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
0 181
1 -2 0 0 0 0 0 0
2 -1.9 0 0 0 0 0 0
3 -1.8 0 0 0 0 0 0
4 -1.7 0 0 0 0 0 0
5 -1.6 0 0 0 0 0 0
6 -1.5 0 0 0 -9.81273e-05 0.000228605 -0.00421138
7 -1.4 0 0 0 -9.81273e-05 0.000228605 -0.00421138
8 -1.3 0 0 0 -9.81273e-05 0.000228605 -0.00421138
9 -1.2 0 0 0 -9.81273e-05 0.000228605 -0.00421138
10 -1.1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
11 -1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
12 -0.9 0 0 0 -9.81273e-05 0.000228605 -0.00421138
13 -0.8 0 0 0 -9.81273e-05 0.000228605 -0.00421138
14 -0.7 0 0 0 -0.000370675 -0.00240125 -0.26848
15 -0.6 0 0 0 -0.000370675 -0.00240125 -0.26848
16 -0.5 0 0 0 -0.000370675 -0.00240125 -0.26848
17 -0.4 0 0 0 -0.000370675 -0.00240125 -0.26848
18 -0.3 0 0 0 -0.000370675 -0.00240125 -0.26848
19 -0.2 0 0 0 -0.000370675 -0.00240125 -0.26848
20 -0.1 0 0 0 -0.000370675 -0.00240125 -0.26848
21 0 0 0 0 -0.000370675 -0.00240125 -0.26848
22 0.1 0 0 0 0.190761 -0.491728 0.287704
23 0.2 0 0 0 0.190761 -0.491728 0.287704
24 0.3 0 0 0 0.190761 -0.491728 0.287704
25 0.4 0 0 0 0.190761 -0.491728 0.287704
26 0.5 0 0 0 0.190761 -0.491728 0.287704
27 0.6 0 0 0 0.190761 -0.491728 0.287704
28 0.7 0 0 0 0.190761 -0.491728 0.287704
29 0.8 0 0 0 -0.181602 -0.198457 -0.0964774
30 0.9 0 0 0 -0.15138 0.183353 0.206848
31 1 0 0 0 0.174362 1.27701 0.600545
32 1.1 0 0 0 0.160987 0.563442 0.494994
33 1.2 0 0 0 0.218876 0.59796 0.398527
34 1.3 0 0 0 0.187614 0.558909 0.372353
35 1.4 0 0 0 0.118586 0.410013 0.331945
36 1.5 0 0 0 -0.0514208 0.40381 0.128097
37 1.6 3.08628 0.241189 5.90817 -0.198262 0.324128 -0.0449302
38 1.7 0 0 0 -0.104542 0.256677 -0.332854
39 1.8 0.222123 2.43524 1.10089 -0.324638 -0.168682 -1.06238
40 1.9 0 0 0 -0.175732 -0.186846 -0.163062
41 2 0 0 0 -0.137995 0.0920401 -0.260106
42 2.1 -0.179621 -2.59775 1.80077 -0.480624 -0.0439511 -0.0824913
43 2.2 0 0 0 -0.499868 -0.0106185 -0.108924
44 2.3 0 0 0 -0.703301 0.124555 -0.0880158
45 2.4 0 0 0 -0.581211 -0.244281 -0.250071
46 2.5 1.05274 -2.86043 3.36339 -0.575104 -0.148715 -0.249092
47 2.6 0 0 0 0.66061 -0.157649 -0.357141
48 2.7 0 0 0 0.299971 -0.302298 -0.572714
49 2.8 0 0 0 0.33107 -0.201699 -0.470466
50 2.9 0 0 0 0.822686 1.08427 -0.390511
51 3 0 0 0 0.716428 0.750998 -0.698174
52 3.1 0.805189 0.571878 4.31938 0.121891 0.922727 -0.932582
53 3.2 0 0 0 0.0442642 1.02537 -1.03066
54 3.3 2.54289 -1.93701 4.88355 0.0731321 1.09091 -0.83075
55 3.4 0 0 0 0.426589 0.821174 -0.765855
56 3.5 0 0 0 0.445135 0.299996 -1.48972
57 3.6 0 0 0 0.362916 -1.28673 -0.853897
58 3.7 0.952867 -1.07044 1.04141 0.12517 -1.00353 -0.785272
59 3.8 0.617661 0.991499 1.80973 -0.182369 -1.04057 -1.00435
60 3.9 0.60295 -2.41888 3.98011 0.0347345 -1.01302 -0.88314
61 4 -2.97421 -2.01531 2.98586 0.43463 -0.465643 -0.801128
62 4.1 -3.23318 -3.31281 0.956525 0.732752 0.140718 -1.10583
63 4.2 0 0 0 0.969872 0.298566 -0.823464
64 4.3 0 0 0 0.7707 0.557002 -0.836549
65 4.4 0 0 0 0.395828 0.66755 -1.53454
66 4.5 0 0 0 0.104451 0.46777 -1.32358
67 4.6 0 0 0 0.402084 0.464983 -1.22051
68 4.7 0 0 0 0.352808 0.0794986 -1.31292
69 4.8 0 0 0 0.0215512 0.284343 -0.975326
70 4.9 0 0 0 -0.133637 0.250925 -1.33918
71 5 0 0 0 -0.066208 0.104514 -1.27412
72 5.1 0 0 0 -0.184391 0.479805 -1.15139
73 5.2 0 0 0 -0.200251 0.527142 -1.34307
74 5.3 0 0 0 0.043532 -0.0788824 -0.998406
75 5.4 0 0 0 -0.531846 0.126289 -1.05818
76 5.5 0 0 0 -0.259593 0.0818463 -1.58939
77 5.6 0 0 0 -0.373828 -0.343977 -1.50908
78 5.7 -0.294161 -1.07567 3.46536 -0.0644873 -0.424333 -1.28548
79 5.8 0 0 0 -0.293233 -0.201133 -1.19085
80 5.9 0.961568 -1.44949 2.42101 -0.632816 -0.0669315 -0.85119
81 6 0 0 0 -0.0559892 -0.0194478 -1.04541
82 6.1 0 0 0 -0.339753 0.286693 -1.24366
83 6.2 0 0 0 -0.376208 0.444053 -1.7662
84 6.3 0 0 0 -0.718923 0.555398 -1.93862
85 6.4 0 0 0 -1.10631 0.263525 -1.79723
86 6.5 0 0 0 -0.217948 -0.0489491 -2.07833
87 6.6 0 0 0 -0.376248 -0.0588682 -2.45322
88 6.7 -2.12742 4.22609 2.36568 -0.236703 -0.279582 -1.56434
89 6.8 0.869072 -0.141389 3.92123 0.0540986 -0.00271606 -0.930143
90 6.9 0 0 0 1.08829 -1.11737 -0.808187
91 7 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
92 7.1 0 0 0 1.03324 -0.470631 -0.486767
93 7.2 0 0 0 0.950164 -0.112451 -0.479409
94 7.3 -2.66121 -0.326607 7.83093 0.359 -0.482493 0.154384
95 7.4 0 0 0 0.359089 -1.12337 0.409711
96 7.5 -1.88971 1.34806 3.56893 0.394677 -1.0109 0.548348
97 7.6 -1.34494 -0.896214 2.06959 0.231398 -0.728529 0.313513
98 7.7 0 0 0 0.415681 -0.45268 0.507181
99 7.8 0 0 0 0.259423 -0.11638 0.464208
100 7.9 -1.97572 -1.20836 3.95731 0.252257 -0.0845701 -0.249345
101 8 0 0 0 0.0688154 0.290386 -0.462467
102 8.1 0.25925 -0.458269 3.33086 0.360399 -0.0409494 -0.656911
103 8.2 0 0 0 -0.0587033 0.347698 -0.340604
104 8.3 0 0 0 -0.377192 0.153096 -0.914654
105 8.4 0 0 0 -0.431553 0.274996 -0.946252
106 8.5 0 0 0 -0.898366 0.146653 -1.36383
107 8.6 0 0 0 -0.889593 0.385951 0.125116
108 8.7 0 0 0 -0.0139171 -0.162302 -0.0287854
109 8.8 0 0 0 -0.266284 -0.148945 0.393533
110 8.9 0 0 0 -0.00920376 -0.0770818 0.334642
111 9 0 0 0 -0.0949156 0.0113352 -0.0761263
112 9.1 0 0 0 0.0688045 0.104558 -0.101891
113 9.2 3.79773 0.0255401 3.75032 0.419832 0.295402 0.652533
114 9.3 0 0 0 0.594267 0.70396 0.836434
115 9.4 0 0 0 0.174722 1.00483 1.42787
116 9.5 0 0 0 0.0626835 0.518952 0.269158
117 9.6 0 0 0 -0.302859 -0.265212 -0.0145578
118 9.7 0 0 0 -0.114026 -0.201336 -0.539522
119 9.8 0 0 0 0.104008 -0.30236 -0.0789062
120 9.9 0 0 0 -0.0482778 -0.553118 0.45214
121 10 0 0 0 -0.0554938 -0.402692 0.141112
122 10.1 0 0 0 0.174338 0.556958 -0.0922154
123 10.2 0 0 0 -1.06045 0.541565 -0.0409312
124 10.3 0 0 0 -1.20782 0.464574 -0.413871
125 10.4 0 0 0 -0.891701 0.327653 -0.286438
126 10.5 0 0 0 0.231227 -0.064277 -0.89684
127 10.6 -1.27989 -4.87365 9.40433 0.211278 0.230826 -1.23536
128 10.7 -2.1001 -0.417817 1.17745 0.425856 0.078728 -1.44229
129 10.8 0 0 0 0.30965 0.450884 -1.74985
130 10.9 0 0 0 0.36735 0.990032 -1.19971
131 11 0.253834 -1.84303 3.91828 1.01826 0.0660896 -0.481086
132 11.1 0 0 0 0.744006 0.0906555 -0.897417
133 11.2 0 0 0 0.339073 0.361038 -0.545084
134 11.3 -1.9974 -0.431998 3.46296 0.611295 0.17282 0.0341483
135 11.4 0 0 0 -0.491432 -0.958871 1.28001
136 11.5 0 0 0 0.0431048 -1.50924 1.24037
137 11.6 0 0 0 -0.684419 -0.0163951 1.06179
138 11.7 0 0 0 -0.425278 -0.127741 0.757298
139 11.8 -2.09164 0.00894897 2.22812 -0.0955178 -0.310572 0.661289
140 11.9 0 0 0 0.156959 -0.233409 0.802568
141 12 0 0 0 -0.05541 -0.346448 0.541571
142 12.1 0 0 0 0.706767 0.182767 0.25767
143 12.2 0 0 0 0.4791 0.464612 -0.212887
144 12.3 0 0 0 0.81454 0.440323 -0.461359
145 12.4 0 0 0 -0.110025 0.200698 -0.996706
146 12.5 0 0 0 -0.149791 0.165599 -1.02233
147 12.6 0 0 0 -0.170933 0.0644682 -0.866174
148 12.7 0 0 0 -0.122869 -0.0196287 -0.801348
149 12.8 0 0 0 -0.0693832 -0.0673091 -0.382802
150 12.9 0 0 0 -0.0693832 -0.0673091 -0.382802
151 13 0 0 0 -0.0693832 -0.0673091 -0.382802
152 13.1 0 0 0 -0.0693832 -0.0673091 -0.382802
153 13.2 0 0 0 -0.0693832 -0.0673091 -0.382802
154 13.3 0 0 0 -0.0693832 -0.0673091 -0.382802
155 13.4 0 0 0 -0.0693832 -0.0673091 -0.382802
156 13.5 0 0 0 -0.000502433 0.000137492 -0.227425
157 13.6 0 0 0 -0.000502433 0.000137492 -0.227425
158 13.7 0 0 0 -0.000502433 0.000137492 -0.227425
159 13.8 0 0 0 -0.000502433 0.000137492 -0.227425
160 13.9 0 0 0 -0.000502433 0.000137492 -0.227425
161 14 0 0 0 -0.000502433 0.000137492 -0.227425
162 14.1 0 0 0 -0.000502433 0.000137492 -0.227425
163 14.2 0 0 0 -0.000502433 0.000137492 -0.227425
164 14.3 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
165 14.4 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
166 14.5 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
167 14.6 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
168 14.7 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
169 14.8 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
170 14.9 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
171 15 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
172 15.1 0 0 0 0 0 0
173 15.2 0 0 0 0 0 0
174 15.3 0 0 0 0 0 0
175 15.4 0 0 0 0 0 0
176 15.5 0 0 0 0 0 0
177 15.6 0 0 0 0 0 0
178 15.7 0 0 0 0 0 0
179 15.8 0 0 0 0 0 0
180 15.9 0 0 0 0 0 0
181 16 0 0 0 0 0 0

3
examples/USER/misc/mop/mopz0.time.reference Normal file
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@ -0,0 +1,3 @@
# Time-averaged data for fix mopz0t
# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394

25
examples/USER/scafacos/data.NaCl Normal file
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@ -0,0 +1,25 @@
LAMMPS Description
8 atoms
2 atom types
0 1 xlo xhi
0 1 ylo yhi
0 1 zlo zhi
Masses
1 22.98976928
2 35.45
Atoms
1 2 1 0.25 0.25 0.25
2 1 -1 0.75 0.25 0.25
3 1 -1 0.25 0.75 0.25
4 2 1 0.75 0.75 0.25
5 1 -1 0.25 0.25 0.75
6 2 1 0.75 0.25 0.75
7 2 1 0.25 0.75 0.75
8 1 -1 0.75 0.75 0.75

316
examples/USER/scafacos/data.cloud_wall Normal file
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@ -0,0 +1,316 @@
LAMMPS Description
300 atoms
1 atom types
0 10 xlo xhi
0 10 ylo yhi
0 10 zlo zhi
Masses
1 1.0
Atoms
1 1 1 0 0 4.5
2 1 -1 0 0 5.5
3 1 1 0 1 4.5
4 1 -1 0 1 5.5
5 1 1 0 2 4.5
6 1 -1 0 2 5.5
7 1 1 0 3 4.5
8 1 -1 0 3 5.5
9 1 1 0 4 4.5
10 1 -1 0 4 5.5
11 1 1 0 5 4.5
12 1 -1 0 5 5.5
13 1 1 0 6 4.5
14 1 -1 0 6 5.5
15 1 1 0 7 4.5
16 1 -1 0 7 5.5
17 1 1 0 8 4.5
18 1 -1 0 8 5.5
19 1 1 0 9 4.5
20 1 -1 0 9 5.5
21 1 1 1 0 4.5
22 1 -1 1 0 5.5
23 1 1 1 1 4.5
24 1 -1 1 1 5.5
25 1 1 1 2 4.5
26 1 -1 1 2 5.5
27 1 1 1 3 4.5
28 1 -1 1 3 5.5
29 1 1 1 4 4.5
30 1 -1 1 4 5.5
31 1 1 1 5 4.5
32 1 -1 1 5 5.5
33 1 1 1 6 4.5
34 1 -1 1 6 5.5
35 1 1 1 7 4.5
36 1 -1 1 7 5.5
37 1 1 1 8 4.5
38 1 -1 1 8 5.5
39 1 1 1 9 4.5
40 1 -1 1 9 5.5
41 1 1 2 0 4.5
42 1 -1 2 0 5.5
43 1 1 2 1 4.5
44 1 -1 2 1 5.5
45 1 1 2 2 4.5
46 1 -1 2 2 5.5
47 1 1 2 3 4.5
48 1 -1 2 3 5.5
49 1 1 2 4 4.5
50 1 -1 2 4 5.5
51 1 1 2 5 4.5
52 1 -1 2 5 5.5
53 1 1 2 6 4.5
54 1 -1 2 6 5.5
55 1 1 2 7 4.5
56 1 -1 2 7 5.5
57 1 1 2 8 4.5
58 1 -1 2 8 5.5
59 1 1 2 9 4.5
60 1 -1 2 9 5.5
61 1 1 3 0 4.5
62 1 -1 3 0 5.5
63 1 1 3 1 4.5
64 1 -1 3 1 5.5
65 1 1 3 2 4.5
66 1 -1 3 2 5.5
67 1 1 3 3 4.5
68 1 -1 3 3 5.5
69 1 1 3 4 4.5
70 1 -1 3 4 5.5
71 1 1 3 5 4.5
72 1 -1 3 5 5.5
73 1 1 3 6 4.5
74 1 -1 3 6 5.5
75 1 1 3 7 4.5
76 1 -1 3 7 5.5
77 1 1 3 8 4.5
78 1 -1 3 8 5.5
79 1 1 3 9 4.5
80 1 -1 3 9 5.5
81 1 1 4 0 4.5
82 1 -1 4 0 5.5
83 1 1 4 1 4.5
84 1 -1 4 1 5.5
85 1 1 4 2 4.5
86 1 -1 4 2 5.5
87 1 1 4 3 4.5
88 1 -1 4 3 5.5
89 1 1 4 4 4.5
90 1 -1 4 4 5.5
91 1 1 4 5 4.5
92 1 -1 4 5 5.5
93 1 1 4 6 4.5
94 1 -1 4 6 5.5
95 1 1 4 7 4.5
96 1 -1 4 7 5.5
97 1 1 4 8 4.5
98 1 -1 4 8 5.5
99 1 1 4 9 4.5
100 1 -1 4 9 5.5
101 1 1 5 0 4.5
102 1 -1 5 0 5.5
103 1 1 5 1 4.5
104 1 -1 5 1 5.5
105 1 1 5 2 4.5
106 1 -1 5 2 5.5
107 1 1 5 3 4.5
108 1 -1 5 3 5.5
109 1 1 5 4 4.5
110 1 -1 5 4 5.5
111 1 1 5 5 4.5
112 1 -1 5 5 5.5
113 1 1 5 6 4.5
114 1 -1 5 6 5.5
115 1 1 5 7 4.5
116 1 -1 5 7 5.5
117 1 1 5 8 4.5
118 1 -1 5 8 5.5
119 1 1 5 9 4.5
120 1 -1 5 9 5.5
121 1 1 6 0 4.5
122 1 -1 6 0 5.5
123 1 1 6 1 4.5
124 1 -1 6 1 5.5
125 1 1 6 2 4.5
126 1 -1 6 2 5.5
127 1 1 6 3 4.5
128 1 -1 6 3 5.5
129 1 1 6 4 4.5
130 1 -1 6 4 5.5
131 1 1 6 5 4.5
132 1 -1 6 5 5.5
133 1 1 6 6 4.5
134 1 -1 6 6 5.5
135 1 1 6 7 4.5
136 1 -1 6 7 5.5
137 1 1 6 8 4.5
138 1 -1 6 8 5.5
139 1 1 6 9 4.5
140 1 -1 6 9 5.5
141 1 1 7 0 4.5
142 1 -1 7 0 5.5
143 1 1 7 1 4.5
144 1 -1 7 1 5.5
145 1 1 7 2 4.5
146 1 -1 7 2 5.5
147 1 1 7 3 4.5
148 1 -1 7 3 5.5
149 1 1 7 4 4.5
150 1 -1 7 4 5.5
151 1 1 7 5 4.5
152 1 -1 7 5 5.5
153 1 1 7 6 4.5
154 1 -1 7 6 5.5
155 1 1 7 7 4.5
156 1 -1 7 7 5.5
157 1 1 7 8 4.5
158 1 -1 7 8 5.5
159 1 1 7 9 4.5
160 1 -1 7 9 5.5
161 1 1 8 0 4.5
162 1 -1 8 0 5.5
163 1 1 8 1 4.5
164 1 -1 8 1 5.5
165 1 1 8 2 4.5
166 1 -1 8 2 5.5
167 1 1 8 3 4.5
168 1 -1 8 3 5.5
169 1 1 8 4 4.5
170 1 -1 8 4 5.5
171 1 1 8 5 4.5
172 1 -1 8 5 5.5
173 1 1 8 6 4.5
174 1 -1 8 6 5.5
175 1 1 8 7 4.5
176 1 -1 8 7 5.5
177 1 1 8 8 4.5
178 1 -1 8 8 5.5
179 1 1 8 9 4.5
180 1 -1 8 9 5.5
181 1 1 9 0 4.5
182 1 -1 9 0 5.5
183 1 1 9 1 4.5
184 1 -1 9 1 5.5
185 1 1 9 2 4.5
186 1 -1 9 2 5.5
187 1 1 9 3 4.5
188 1 -1 9 3 5.5
189 1 1 9 4 4.5
190 1 -1 9 4 5.5
191 1 1 9 5 4.5
192 1 -1 9 5 5.5
193 1 1 9 6 4.5
194 1 -1 9 6 5.5
195 1 1 9 7 4.5
196 1 -1 9 7 5.5
197 1 1 9 8 4.5
198 1 -1 9 8 5.5
199 1 1 9 9 4.5
200 1 -1 9 9 5.5
201 1 -1 9.28495 2.13839 8.88019
202 1 1 4.99281 4.17459 9.83905
203 1 -1 4.91265 6.89408 2.39989
204 1 1 4.43647 3.68895 8.86086
205 1 -1 0.659075 7.07271 0.179131
206 1 1 7.791 3.40021 0.969703
207 1 -1 1.18008 3.63874 7.28751
208 1 1 8.51522 5.24681 6.37702
209 1 -1 4.24226 9.60726 3.16084
210 1 1 8.43745 8.23344 9.2883
211 1 -1 8.48509 8.84988 9.43407
212 1 1 2.81127 8.9903 0.00909212
213 1 -1 6.38283 6.20858 9.92482
214 1 1 4.59962 5.7925 7.52571
215 1 -1 7.03797 7.09336 8.15957
216 1 1 6.68103 8.04734 7.95661
217 1 -1 2.531 8.47145 1.6209
218 1 1 6.71915 8.79876 9.59581
219 1 -1 4.96758 0.0381298 0.827927
220 1 1 9.22955 1.04572 0.84722
221 1 -1 2.3224 2.57084 8.07306
222 1 1 1.94283 3.17375 3.92051
223 1 -1 2.34735 1.91295 1.29127
224 1 1 3.33928 3.30688 0.892089
225 1 -1 1.19738 4.40402 8.70835
226 1 1 7.44541 4.94803 8.28211
227 1 -1 5.93272 1.18886 1.56518
228 1 1 8.50709 8.70343 1.24939
229 1 -1 5.54016 3.38865 8.61698
230 1 1 9.47644 0.573085 3.05941
231 1 -1 9.39695 4.46542 1.84205
232 1 1 3.52268 5.60212 0.333999
233 1 -1 3.69009 9.40954 6.10446
234 1 1 3.96836 6.15307 7.57803
235 1 -1 2.02535 0.0418407 3.21642
236 1 1 2.97488 8.79711 8.33242
237 1 -1 2.4122 1.79458 3.04173
238 1 1 9.72355 3.67773 1.52435
239 1 -1 8.55216 6.1623 1.53201
240 1 1 4.98973 2.41459 9.84381
241 1 -1 8.8901 5.9006 1.97649
242 1 1 9.09932 2.23783 1.42554
243 1 -1 6.70722 8.21769 1.21953
244 1 1 6.83768 0.84508 3.25165
245 1 -1 0.222115 3.07945 0.51825
246 1 1 0.503918 9.34932 6.25278
247 1 -1 0.803159 8.7017 9.46211
248 1 1 4.88636 5.00147 9.65639
249 1 -1 1.62258 0.767285 9.63596
250 1 1 2.70143 3.01111 7.74859
251 1 -1 4.41574 5.31824 0.538729
252 1 1 1.64724 5.18097 3.59205
253 1 -1 2.33672 3.21408 6.6081
254 1 1 7.46603 1.53668 9.09844
255 1 -1 3.61269 8.44556 6.99789
256 1 1 6.95465 6.83045 9.31002
257 1 -1 5.91831 9.01549 3.4626
258 1 1 6.56503 8.42229 3.27105
259 1 -1 4.50822 9.59753 3.47025
260 1 1 4.17357 5.27384 7.34774
261 1 -1 7.70968 6.5292 3.54779
262 1 1 4.7977 4.94239 6.24947
263 1 -1 9.24016 9.36994 6.71263
264 1 1 7.36888 8.75922 0.52403
265 1 -1 9.92895 5.87551 6.21586
266 1 1 3.86308 6.71601 9.69083
267 1 -1 8.90048 0.298719 0.573852
268 1 1 6.58753 6.67768 1.83984
269 1 -1 8.672 0.367497 2.21864
270 1 1 3.44519 3.30359 6.52249
271 1 -1 7.24717 3.25113 3.41567
272 1 1 9.53447 5.81336 1.79208
273 1 -1 1.01722 6.42534 0.715
274 1 1 3.58808 4.92392 7.00979
275 1 -1 1.21399 3.56951 6.34505
276 1 1 3.50336 0.942722 2.76989
277 1 -1 9.45475 6.06299 0.659023
278 1 1 3.44464 4.03075 6.20179
279 1 -1 0.949331 5.40183 8.51385
280 1 1 6.41118 2.62135 2.31132
281 1 -1 3.58837 9.78355 7.04966
282 1 1 9.2267 3.19593 2.10384
283 1 -1 1.83092 2.35627 3.93061
284 1 1 4.97203 4.92287 1.8049
285 1 -1 7.4097 4.757 8.604
286 1 1 0.746575 7.69038 0.89134
287 1 -1 8.54862 6.59135 2.18888
288 1 1 2.18747 4.82994 0.761718
289 1 -1 5.71622 2.51116 6.85522
290 1 1 6.95554 1.83187 8.31157
291 1 -1 7.31818 6.60081 2.63208
292 1 1 0.744495 2.73429 9.86022
293 1 -1 5.1573 8.70962 2.53418
294 1 1 2.40385 1.54057 1.9297
295 1 -1 3.42609 2.25856 2.28437
296 1 1 6.66173 3.70851 9.70052
297 1 -1 7.88966 1.4343 8.91223
298 1 1 3.91118 5.22253 6.29642
299 1 -1 9.17618 3.98313 9.82158
300 1 1 4.95424 5.93521 1.3652

1016
examples/USER/scafacos/data.hammersley_sphere Normal file
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examples/USER/scafacos/in.scafacos Normal file
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# Point dipoles in a 2d box
units lj
atom_style full
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p3m 0.001
kspace_style scafacos tolerance field
timestep 0.005
thermo 10
run 100

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