forked from lijiext/lammps
Merge remote-tracking branch 'origin/master' into exaalt
This commit is contained in:
Christoph Junghans
commit
2f6be88c4a
|
|
@ -0,0 +1,21 @@
|
|||
# This file contains file patterns that triggers automatic
|
||||
# code review requests from users that are owners of these files
|
||||
# Order matters, the last match has the highest precedence
|
||||
|
||||
# library folders
|
||||
lib/colvars/* @giacomofiorin
|
||||
lib/compress/* @akohlmey
|
||||
lib/kokkos/* @stanmoore1
|
||||
lib/molfile/* @akohlmey
|
||||
lib/qmmm/* @akohlmey
|
||||
lib/vtk/* @rbberger
|
||||
|
||||
# packages
|
||||
src/KOKKOS @stanmoore1
|
||||
src/USER-CGSDK @akohlmey
|
||||
src/USER-COLVARS @giacomofiorin
|
||||
src/USER-OMP @akohlmey
|
||||
src/USER-QMMM @akohlmey
|
||||
|
||||
# tools
|
||||
tools/msi2lmp/* @akohlmey
|
||||
|
|
@ -32,3 +32,11 @@ log.cite
|
|||
.Trashes
|
||||
ehthumbs.db
|
||||
Thumbs.db
|
||||
|
||||
#cmake
|
||||
/build*
|
||||
/CMakeCache.txt
|
||||
/CMakeFiles/
|
||||
/Makefile
|
||||
/cmake_install.cmake
|
||||
/lmp
|
||||
|
|
|
|||
|
|
@ -0,0 +1,547 @@
|
|||
########################################
|
||||
# CMake build system
|
||||
# This file is part of LAMMPS
|
||||
# Created by Christoph Junghans and Richard Berger
|
||||
cmake_minimum_required(VERSION 3.1)
|
||||
|
||||
project(lammps)
|
||||
set(SOVERSION 0)
|
||||
set(LAMMPS_SOURCE_DIR ${CMAKE_SOURCE_DIR}/../src)
|
||||
set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_SOURCE_DIR}/../lib)
|
||||
set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib)
|
||||
|
||||
#To not conflict with old Makefile build system, we build everything here
|
||||
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
|
||||
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
|
||||
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
|
||||
|
||||
# Cmake modules/macros are in a subdirectory to keep this file cleaner
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/Modules)
|
||||
|
||||
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
#release comes with -O3 by default
|
||||
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
|
||||
foreach(STYLE_FILE style_angle.h style_atom.h style_body.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h
|
||||
style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_nbin.h style_npair.h style_nstencil.h
|
||||
style_ntopo.h style_pair.h style_reader.h style_region.h)
|
||||
if(EXISTS ${LAMMPS_SOURCE_DIR}/${STYLE_FILE})
|
||||
message(FATAL_ERROR "There is a ${STYLE_FILE} in ${LAMMPS_SOURCE_DIR}, please clean up the source directory first")
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
enable_language(CXX)
|
||||
|
||||
######################################################################
|
||||
# compiler tests
|
||||
# these need ot be done early (before further tests).
|
||||
#####################################################################
|
||||
include(CheckCCompilerFlag)
|
||||
|
||||
########################################################################
|
||||
# User input options #
|
||||
########################################################################
|
||||
option(BUILD_SHARED_LIBS "Build shared libs" OFF)
|
||||
option(INSTALL_LIB "Install lammps library and header" ON)
|
||||
include(GNUInstallDirs)
|
||||
|
||||
set(LAMMPS_LINK_LIBS)
|
||||
option(ENABLE_MPI "Build MPI version" OFF)
|
||||
if(ENABLE_MPI)
|
||||
find_package(MPI REQUIRED)
|
||||
include_directories(${MPI_C_INCLUDE_PATH})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
|
||||
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
|
||||
if(LAMMPS_LONGLONG_TO_LONG)
|
||||
add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
|
||||
endif()
|
||||
else()
|
||||
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
|
||||
list(APPEND LIB_SOURCES ${MPI_SOURCES})
|
||||
include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
|
||||
endif()
|
||||
|
||||
set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
|
||||
set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
|
||||
add_definitions(-D${LAMMPS_SIZE_LIMIT})
|
||||
|
||||
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
|
||||
add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
|
||||
|
||||
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_definitions(-DLAMMPS_EXCEPTIONS)
|
||||
endif()
|
||||
|
||||
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
|
||||
|
||||
option(ENABLE_TESTING "Enable testing" OFF)
|
||||
if(ENABLE_TESTING)
|
||||
enable_testing()
|
||||
endif(ENABLE_TESTING)
|
||||
|
||||
option(ENABLE_ALL "Build all default packages" OFF)
|
||||
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
|
||||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
|
||||
REAX REPLICA RIGID SHOCK SNAP SRD)
|
||||
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS
|
||||
USER-ATC USER-AWPMD USER-CGDNA
|
||||
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-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
|
||||
USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
|
||||
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
|
||||
foreach(PKG ${DEFAULT_PACKAGES})
|
||||
option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
|
||||
endforeach()
|
||||
foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
|
||||
option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
|
||||
endforeach()
|
||||
|
||||
macro(pkg_depends PKG1 PKG2)
|
||||
if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
|
||||
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
|
||||
endif()
|
||||
endmacro()
|
||||
|
||||
pkg_depends(MPIIO MPI)
|
||||
pkg_depends(QEQ MANYBODY)
|
||||
pkg_depends(USER-ATC MANYBODY)
|
||||
pkg_depends(USER-H5MD MPI)
|
||||
pkg_depends(USER-LB MPI)
|
||||
pkg_depends(USER-MISC MANYBODY)
|
||||
pkg_depends(USER-PHONON KSPACE)
|
||||
|
||||
if(ENABLE_BODY AND ENABLE_POEMS)
|
||||
message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
|
||||
endif()
|
||||
|
||||
######################################################
|
||||
# packages with special compiler needs or external libs
|
||||
######################################################
|
||||
if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM)
|
||||
enable_language(Fortran)
|
||||
endif()
|
||||
|
||||
if(ENABLE_KOKKOS OR ENABLE_MSCG)
|
||||
# starting with CMake 3.1 this is all you have to do to enforce C++11
|
||||
set(CMAKE_CXX_STANDARD 11) # C++11...
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
|
||||
set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
|
||||
find_package(OpenMP REQUIRED)
|
||||
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
|
||||
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
|
||||
endif()
|
||||
|
||||
if(ENABLE_KSPACE)
|
||||
set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
|
||||
set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
|
||||
if(NOT FFT STREQUAL "KISSFFT")
|
||||
find_package(${FFT} REQUIRED)
|
||||
add_definitions(-DFFT_${FFT})
|
||||
include_directories(${${FFT}_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
|
||||
endif()
|
||||
set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT")
|
||||
set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY)
|
||||
if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY")
|
||||
add_definitions(-D${PACK_OPTIMIZATION})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
if(ENABLE_MISC)
|
||||
option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
|
||||
if(LAMMPS_XDR)
|
||||
add_definitions(-DLAMMPS_XDR)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP)
|
||||
find_package(LAPACK)
|
||||
if(LAPACK_FOUND)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${LAPACK_LIBRARIES})
|
||||
else()
|
||||
enable_language(Fortran)
|
||||
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
|
||||
list(APPEND LIB_SOURCES ${LAPACK_SOURCES})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
if(ENABLE_PYTHON)
|
||||
find_package(PythonInterp REQUIRED)
|
||||
find_package(PythonLibs REQUIRED)
|
||||
add_definitions(-DLMP_PYTHON)
|
||||
include_directories(${PYTHON_INCLUDE_DIR})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
|
||||
if(NOT PYTHON_INSTDIR)
|
||||
execute_process(COMMAND ${PYTHON_EXECUTABLE}
|
||||
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
|
||||
OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
install(FILES ${CMAKE_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
|
||||
if(NOT BUILD_SHARED_LIBS)
|
||||
message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
find_package(JPEG)
|
||||
if(JPEG_FOUND)
|
||||
add_definitions(-DLAMMPS_JPEG)
|
||||
include_directories(${JPEG_INCLUDE_DIR})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
|
||||
endif()
|
||||
|
||||
find_package(PNG)
|
||||
find_package(ZLIB)
|
||||
if(PNG_FOUND AND ZLIB_FOUND)
|
||||
include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
|
||||
add_definitions(-DLAMMPS_PNG)
|
||||
endif()
|
||||
|
||||
find_program(GZIP_EXECUTABLE gzip)
|
||||
find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
|
||||
if(GZIP_FOUND)
|
||||
add_definitions(-DLAMMPS_GZIP)
|
||||
endif()
|
||||
|
||||
find_program(FFMPEG_EXECUTABLE ffmpeg)
|
||||
find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
|
||||
if(FFMPEG_FOUND)
|
||||
add_definitions(-DLAMMPS_FFMPEG)
|
||||
endif()
|
||||
|
||||
if(ENABLE_VORONOI)
|
||||
find_package(VORO REQUIRED) #some distros
|
||||
include_directories(${VORO_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-MOLFILE)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_DL_LIBS})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-NETCDF)
|
||||
find_package(NetCDF REQUIRED)
|
||||
include_directories(NETCDF_INCLUDE_DIR)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
|
||||
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-SMD)
|
||||
find_package(Eigen3 REQUIRED)
|
||||
include_directories(${EIGEN3_INCLUDE_DIR})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-QUIP)
|
||||
find_package(QUIP REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-QMMM)
|
||||
find_package(QE REQUIRED)
|
||||
include_directories(${QE_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-AWPMD)
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact
|
||||
${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-H5MD)
|
||||
find_package(HDF5 REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${HDF5_LIBRARIES})
|
||||
include_directories(${HDF5_INCLUDE_DIRS} ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-VTK)
|
||||
find_package(VTK REQUIRED NO_MODULE)
|
||||
include(${VTK_USE_FILE})
|
||||
add_definitions(-DLAMMPS_VTK)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_KIM)
|
||||
find_package(KIM REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
|
||||
include_directories(${KIM_INCLUDE_DIRS})
|
||||
endif()
|
||||
|
||||
if(ENABLE_MSCG)
|
||||
find_package(GSL REQUIRED)
|
||||
set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
|
||||
set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
|
||||
set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
|
||||
if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
|
||||
if(NOT EXISTS ${MSCG_TARBALL})
|
||||
message(STATUS "Downloading ${MSCG_TARBALL}")
|
||||
file(DOWNLOAD
|
||||
https://github.com/uchicago-voth/MSCG-release/archive/master.zip
|
||||
${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
|
||||
endif()
|
||||
message(STATUS "Unpacking ${MSCG_TARBALL}")
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
|
||||
WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
|
||||
endif()
|
||||
file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${MSCG_SOURCES})
|
||||
foreach(MSCG_SOURCE ${MSCG_SOURCES})
|
||||
set_property(SOURCE ${MSCG_SOURCE} APPEND PROPERTY COMPILE_DEFINITIONS
|
||||
DIMENSION=3 _exclude_gromacs=1)
|
||||
endforeach()
|
||||
include_directories(${LAMMPS_LIB_MSCG_BIN_DIR} ${GSL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
|
||||
endif()
|
||||
|
||||
########################################################################
|
||||
# Basic system tests (standard libraries, headers, functions, types) #
|
||||
########################################################################
|
||||
include(CheckIncludeFile)
|
||||
foreach(HEADER math.h)
|
||||
check_include_file(${HEADER} FOUND_${HEADER})
|
||||
if(NOT FOUND_${HEADER})
|
||||
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
|
||||
endif(NOT FOUND_${HEADER})
|
||||
endforeach(HEADER)
|
||||
|
||||
set(MATH_LIBRARIES "m" CACHE STRING "math library")
|
||||
mark_as_advanced( MATH_LIBRARIES )
|
||||
include(CheckLibraryExists)
|
||||
foreach(FUNC sin cos)
|
||||
check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
|
||||
if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
|
||||
message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
|
||||
endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
|
||||
endforeach(FUNC)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
|
||||
|
||||
######################################
|
||||
# Generate Basic Style files
|
||||
######################################
|
||||
include(StyleHeaderUtils)
|
||||
RegisterStyles(${LAMMPS_SOURCE_DIR})
|
||||
|
||||
##############################################
|
||||
# add sources of enabled packages
|
||||
############################################
|
||||
foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
|
||||
if(ENABLE_${PKG})
|
||||
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
|
||||
|
||||
# detects styles in package and adds them to global list
|
||||
RegisterStyles(${${PKG}_SOURCES_DIR})
|
||||
|
||||
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
|
||||
include_directories(${${PKG}_SOURCES_DIR})
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
##############################################
|
||||
# add lib sources of (simple) enabled packages
|
||||
############################################
|
||||
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
|
||||
USER-MOLFILE USER-QMMM)
|
||||
if(ENABLE_${SIMPLE_LIB})
|
||||
string(REGEX REPLACE "^USER-" "" SIMPLE_LIB "${SIMPLE_LIB}")
|
||||
string(TOLOWER "${SIMPLE_LIB}" INC_DIR)
|
||||
file(GLOB_RECURSE ${SIMPLE_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.F
|
||||
${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${${SIMPLE_LIB}_SOURCES})
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR})
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
######################################################################
|
||||
# packages which selectively include variants based on enabled styles
|
||||
# e.g. accelerator packages
|
||||
######################################################################
|
||||
if(ENABLE_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_nh_omp.cpp
|
||||
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
|
||||
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
|
||||
|
||||
# detects styles which have USER-OMP version
|
||||
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
|
||||
|
||||
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
|
||||
|
||||
list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
|
||||
include_directories(${USER-OMP_SOURCES_DIR})
|
||||
endif()
|
||||
|
||||
if(ENABLE_KOKKOS)
|
||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
|
||||
add_definitions(-DLMP_KOKKOS)
|
||||
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
|
||||
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
|
||||
${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
include_directories(${Kokkos_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS kokkos)
|
||||
|
||||
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
|
||||
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
|
||||
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
|
||||
|
||||
# detects styles which have KOKKOS version
|
||||
RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
|
||||
|
||||
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
|
||||
|
||||
list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
|
||||
include_directories(${KOKKOS_PKG_SOURCES_DIR})
|
||||
endif()
|
||||
|
||||
if(ENABLE_OPT)
|
||||
set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
|
||||
set(OPT_SOURCES)
|
||||
set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
|
||||
|
||||
# detects styles which have OPT version
|
||||
RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
|
||||
|
||||
get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
|
||||
|
||||
list(APPEND LIB_SOURCES ${OPT_SOURCES})
|
||||
include_directories(${OPT_SOURCES_DIR})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-INTEL)
|
||||
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
|
||||
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
|
||||
${USER-INTEL_SOURCES_DIR}/intel_buffers.h
|
||||
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
|
||||
${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
|
||||
${USER-INTEL_SOURCES_DIR}/nbin_intel.h
|
||||
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
|
||||
${USER-INTEL_SOURCES_DIR}/npair_intel.h
|
||||
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
|
||||
${USER-INTEL_SOURCES_DIR}/intel_simd.h
|
||||
${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
|
||||
|
||||
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
|
||||
|
||||
# detects styles which have USER-INTEL version
|
||||
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
|
||||
|
||||
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
|
||||
|
||||
list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
|
||||
include_directories(${USER-INTEL_SOURCES_DIR})
|
||||
endif()
|
||||
|
||||
if(ENABLE_GPU)
|
||||
find_package(CUDA REQUIRED)
|
||||
find_program(BIN2C bin2c)
|
||||
if(NOT BIN2C)
|
||||
message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
|
||||
endif()
|
||||
include_directories(${CUDA_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||
set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "Lammps gpu precision size")
|
||||
set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
|
||||
add_definitions(-D_${GPU_PREC})
|
||||
add_definitions(-DNV_KERNEL -DUCL_CUDADR)
|
||||
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
|
||||
|
||||
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
|
||||
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h)
|
||||
|
||||
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
|
||||
|
||||
# detects styles which have GPU version
|
||||
RegisterStylesExt(${GPU_SOURCES_DIR} opt GPU_SOURCES)
|
||||
|
||||
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
|
||||
|
||||
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
|
||||
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_SOURCE_DIR}/gpu/*.cu)
|
||||
file(GLOB_RECURSE GPU_NOT_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
|
||||
list(REMOVE_ITEM GPU_LIB_CU ${GPU_NOT_LIB_CU})
|
||||
include_directories(${GPU_SOURCES_DIR} ${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
if(CUDPP_OPT)
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
||||
add_definitions(-DCUDPP_OPT)
|
||||
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(GPU_OBJS ${GPU_LIB_CU} ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>)
|
||||
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
foreach(CU_OBJ ${GPU_OBJS})
|
||||
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
|
||||
string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
|
||||
add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
DEPENDS ${CU_OBJ}
|
||||
COMMENT "Generating ${CU_NAME}_cubin.h")
|
||||
list(APPEND LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
|
||||
if(${CU_NAME} STREQUAL "pppm_d") #pppm_d doesn't get linked into the lib
|
||||
set(CU_FORBIDDEN_OBJ "${CU_OBJ}")
|
||||
endif()
|
||||
endforeach()
|
||||
list(REMOVE_ITEM GPU_OBJS "${CU_FORBIDDEN_OBJ}")
|
||||
list(APPEND LIB_SOURCES ${GPU_SOURCES} ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
|
||||
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
|
||||
endif()
|
||||
|
||||
######################################################
|
||||
# Generate style headers based on global list of
|
||||
# styles registered during package selection
|
||||
######################################################
|
||||
set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
|
||||
|
||||
GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
|
||||
|
||||
include_directories(${LAMMPS_SOURCE_DIR})
|
||||
include_directories(${LAMMPS_STYLE_HEADERS_DIR})
|
||||
|
||||
###########################################
|
||||
# Actually add executable and lib to build
|
||||
############################################
|
||||
add_library(lammps ${LIB_SOURCES})
|
||||
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
if(INSTALL_LIB)
|
||||
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
||||
elseif(BUILD_SHARED_LIBS)
|
||||
message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
|
||||
endif()
|
||||
|
||||
add_executable(lmp ${LMP_SOURCES})
|
||||
target_link_libraries(lmp lammps)
|
||||
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
if(ENABLE_TESTING)
|
||||
add_test(ShowHelp ${CMAKE_CURRENT_BINARY_DIR}/lmp -help)
|
||||
endif()
|
||||
|
||||
##################################
|
||||
# Print package summary
|
||||
##################################
|
||||
foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
|
||||
if(ENABLE_${PKG})
|
||||
message(STATUS "Building package: ${PKG}")
|
||||
endif()
|
||||
endforeach()
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# - Find fftw2
|
||||
# Find the native FFTW2 headers and libraries.
|
||||
#
|
||||
# FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
|
||||
# FFTW2_LIBRARIES - List of libraries when using fftw2.
|
||||
# FFTW2_FOUND - True if fftw2 found.
|
||||
#
|
||||
|
||||
find_path(FFTW2_INCLUDE_DIR fftw.h)
|
||||
|
||||
find_library(FFTW2_LIBRARY NAMES fftw)
|
||||
|
||||
set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
|
||||
set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
# - Find fftw3
|
||||
# Find the native FFTW3 headers and libraries.
|
||||
#
|
||||
# FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
|
||||
# FFTW3_LIBRARIES - List of libraries when using fftw3.
|
||||
# FFTW3_FOUND - True if fftw3 found.
|
||||
#
|
||||
|
||||
find_package(PkgConfig)
|
||||
|
||||
pkg_check_modules(PC_FFTW3 fftw3)
|
||||
find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
|
||||
|
||||
find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
|
||||
|
||||
set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
|
||||
set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# - Find kim
|
||||
# Find the native KIM headers and libraries.
|
||||
#
|
||||
# KIM_INCLUDE_DIRS - where to find kim.h, etc.
|
||||
# KIM_LIBRARIES - List of libraries when using kim.
|
||||
# KIM_FOUND - True if kim found.
|
||||
#
|
||||
|
||||
find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
|
||||
|
||||
find_library(KIM_LIBRARY NAMES kim-api-v1)
|
||||
|
||||
set(KIM_LIBRARIES ${KIM_LIBRARY})
|
||||
set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# - Find mkl
|
||||
# Find the native MKL headers and libraries.
|
||||
#
|
||||
# MKL_INCLUDE_DIRS - where to find mkl.h, etc.
|
||||
# MKL_LIBRARIES - List of libraries when using mkl.
|
||||
# MKL_FOUND - True if mkl found.
|
||||
#
|
||||
|
||||
find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
|
||||
|
||||
find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
|
||||
|
||||
set(MKL_LIBRARIES ${MKL_LIBRARY})
|
||||
set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
# - Find NetCDF
|
||||
# Find the native NetCDF includes and library
|
||||
#
|
||||
# NETCDF_INCLUDE_DIR - user modifiable choice of where netcdf headers are
|
||||
# NETCDF_LIBRARY - user modifiable choice of where netcdf libraries are
|
||||
#
|
||||
# Your package can require certain interfaces to be FOUND by setting these
|
||||
#
|
||||
# NETCDF_CXX - require the C++ interface and link the C++ library
|
||||
# NETCDF_F77 - require the F77 interface and link the fortran library
|
||||
# NETCDF_F90 - require the F90 interface and link the fortran library
|
||||
#
|
||||
# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
|
||||
# more of "CXX;F77;F90".
|
||||
#
|
||||
# When interfaces are requested the user has access to interface specific hints:
|
||||
#
|
||||
# NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
|
||||
# NETCDF_${LANG}_LIBRARY - where to search for interface libraries
|
||||
#
|
||||
# This module returns these variables for the rest of the project to use.
|
||||
#
|
||||
# NETCDF_FOUND - True if NetCDF found including required interfaces (see below)
|
||||
# NETCDF_LIBRARIES - All netcdf related libraries.
|
||||
# NETCDF_INCLUDE_DIRS - All directories to include.
|
||||
# NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
|
||||
# NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
|
||||
#
|
||||
# Normal usage would be:
|
||||
# set (NETCDF_F90 "YES")
|
||||
# find_package (NetCDF REQUIRED)
|
||||
# target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
|
||||
# target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
|
||||
|
||||
#search starting from user editable cache var
|
||||
if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
|
||||
# Already in cache, be silent
|
||||
set (NETCDF_FIND_QUIETLY TRUE)
|
||||
endif ()
|
||||
|
||||
set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
|
||||
if(NETCDF_USE_DEFAULT_PATHS)
|
||||
set(USE_DEFAULT_PATHS "")
|
||||
endif()
|
||||
|
||||
find_path (NETCDF_INCLUDE_DIR netcdf.h
|
||||
HINTS "${NETCDF_DIR}/include")
|
||||
mark_as_advanced (NETCDF_INCLUDE_DIR)
|
||||
set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
|
||||
|
||||
find_library (NETCDF_LIBRARY NAMES netcdf
|
||||
HINTS "${NETCDF_DIR}/lib")
|
||||
mark_as_advanced (NETCDF_LIBRARY)
|
||||
|
||||
set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
|
||||
|
||||
#start finding requested language components
|
||||
set (NetCDF_libs "")
|
||||
set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
|
||||
|
||||
get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
|
||||
set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
|
||||
|
||||
macro (NetCDF_check_interface lang header libs)
|
||||
if (NETCDF_${lang})
|
||||
#search starting from user modifiable cache var
|
||||
find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
|
||||
HINTS "${NETCDF_INCLUDE_DIR}"
|
||||
HINTS "${NETCDF_${lang}_ROOT}/include"
|
||||
${USE_DEFAULT_PATHS})
|
||||
|
||||
find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
|
||||
HINTS "${NetCDF_lib_dirs}"
|
||||
HINTS "${NETCDF_${lang}_ROOT}/lib"
|
||||
${USE_DEFAULT_PATHS})
|
||||
|
||||
mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
|
||||
|
||||
#export to internal varS that rest of project can use directly
|
||||
set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
|
||||
set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
|
||||
|
||||
if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
|
||||
list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
|
||||
list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
|
||||
else ()
|
||||
set (NETCDF_HAS_INTERFACES "NO")
|
||||
message (STATUS "Failed to find NetCDF interface for ${lang}")
|
||||
endif ()
|
||||
endif ()
|
||||
endmacro ()
|
||||
|
||||
list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
|
||||
if (_nextcomp GREATER -1)
|
||||
set (NETCDF_CXX 1)
|
||||
endif ()
|
||||
list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
|
||||
if (_nextcomp GREATER -1)
|
||||
set (NETCDF_F77 1)
|
||||
endif ()
|
||||
list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
|
||||
if (_nextcomp GREATER -1)
|
||||
set (NETCDF_F90 1)
|
||||
endif ()
|
||||
NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
|
||||
NetCDF_check_interface (F77 netcdf.inc netcdff)
|
||||
NetCDF_check_interface (F90 netcdf.mod netcdff)
|
||||
|
||||
#export accumulated results to internal varS that rest of project can depend on
|
||||
list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
|
||||
set (NETCDF_LIBRARIES ${NetCDF_libs})
|
||||
set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
|
||||
|
||||
# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
|
||||
# all listed variables are TRUE
|
||||
include (FindPackageHandleStandardArgs)
|
||||
find_package_handle_standard_args (NetCDF
|
||||
DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
# - Find quantum-espresso
|
||||
# Find the native QE headers and libraries.
|
||||
#
|
||||
# QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
|
||||
# QE_LIBRARIES - List of libraries when using quantum-espresso.
|
||||
# QE_FOUND - True if quantum-espresso found.
|
||||
#
|
||||
|
||||
find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
|
||||
|
||||
find_library(QECOUPLE_LIBRARY NAMES qecouple)
|
||||
find_library(PW_LIBRARY NAMES pw)
|
||||
find_library(QEMOD_LIBRARY NAMES qemod)
|
||||
find_library(QEFFT_LIBRARY NAMES qefft)
|
||||
find_library(QELA_LIBRARY NAMES qela)
|
||||
find_library(CLIB_LIBRARY NAMES clib)
|
||||
find_library(IOTK_LIBRARY NAMES iotk)
|
||||
|
||||
|
||||
set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
|
||||
set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# - Find quip
|
||||
# Find the native QUIP libraries.
|
||||
#
|
||||
# QUIP_LIBRARIES - List of libraries when using fftw3.
|
||||
# QUIP_FOUND - True if fftw3 found.
|
||||
#
|
||||
|
||||
find_library(QUIP_LIBRARY NAMES quip)
|
||||
|
||||
set(QUIP_LIBRARIES ${QUIP_LIBRARY})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
|
||||
|
||||
mark_as_advanced(QUIP_LIBRARY)
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
# - Find voro++
|
||||
# Find the native VORO headers and libraries.
|
||||
#
|
||||
# VORO_INCLUDE_DIRS - where to find voro++.hh, etc.
|
||||
# VORO_LIBRARIES - List of libraries when using voro++.
|
||||
# VORO_FOUND - True if voro++ found.
|
||||
#
|
||||
|
||||
find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
|
||||
|
||||
find_library(VORO_LIBRARY NAMES voro++)
|
||||
|
||||
set(VORO_LIBRARIES ${VORO_LIBRARY})
|
||||
set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )
|
||||
|
|
@ -0,0 +1,132 @@
|
|||
function(FindStyleHeaders path style_class file_pattern headers)
|
||||
file(GLOB files "${path}/${file_pattern}*.h")
|
||||
get_property(hlist GLOBAL PROPERTY ${headers})
|
||||
|
||||
foreach(file_name ${files})
|
||||
file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
|
||||
if(is_style)
|
||||
list(APPEND hlist ${file_name})
|
||||
endif()
|
||||
endforeach()
|
||||
set_property(GLOBAL PROPERTY ${headers} "${hlist}")
|
||||
endfunction(FindStyleHeaders)
|
||||
|
||||
function(FindStyleHeadersExt path style_class extension headers sources)
|
||||
get_property(hlist GLOBAL PROPERTY ${headers})
|
||||
get_property(slist GLOBAL PROPERTY ${sources})
|
||||
set(ext_list)
|
||||
get_filename_component(abs_path "${path}" ABSOLUTE)
|
||||
|
||||
foreach(file_name ${hlist})
|
||||
get_filename_component(basename ${file_name} NAME_WE)
|
||||
set(ext_file_name "${abs_path}/${basename}_${extension}.h")
|
||||
if(EXISTS "${ext_file_name}")
|
||||
file(STRINGS ${ext_file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
|
||||
if(is_style)
|
||||
list(APPEND ext_list ${ext_file_name})
|
||||
|
||||
set(source_file_name "${abs_path}/${basename}_${extension}.cpp")
|
||||
if(EXISTS "${source_file_name}")
|
||||
list(APPEND slist ${source_file_name})
|
||||
endif()
|
||||
endif()
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
list(APPEND hlist ${ext_list})
|
||||
set_property(GLOBAL PROPERTY ${headers} "${hlist}")
|
||||
set_property(GLOBAL PROPERTY ${sources} "${slist}")
|
||||
endfunction(FindStyleHeadersExt)
|
||||
|
||||
function(CreateStyleHeader path filename)
|
||||
math(EXPR N "${ARGC}-2")
|
||||
|
||||
set(temp "")
|
||||
if(N GREATER 0)
|
||||
math(EXPR ARG_END "${ARGC}-1")
|
||||
|
||||
foreach(IDX RANGE 2 ${ARG_END})
|
||||
list(GET ARGV ${IDX} FNAME)
|
||||
get_filename_component(FNAME ${FNAME} NAME)
|
||||
set(temp "${temp}#include \"${FNAME}\"\n")
|
||||
endforeach()
|
||||
endif()
|
||||
message(STATUS "Generating ${filename}...")
|
||||
file(WRITE "${path}/${filename}.tmp" "${temp}" )
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
|
||||
endfunction(CreateStyleHeader)
|
||||
|
||||
function(GenerateStyleHeader path property style)
|
||||
get_property(files GLOBAL PROPERTY ${property})
|
||||
#message("${property} = ${files}")
|
||||
CreateStyleHeader("${path}" "style_${style}.h" ${files})
|
||||
endfunction(GenerateStyleHeader)
|
||||
|
||||
function(RegisterStyles search_path)
|
||||
FindStyleHeaders(${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(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
|
||||
FindStyleHeaders(${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} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
|
||||
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
|
||||
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor
|
||||
FindStyleHeaders(${search_path} NSTENCIL_CLASS nstencil_ NSTENCIL ) # nstencil ) # neighbor
|
||||
FindStyleHeaders(${search_path} NTOPO_CLASS ntopo_ NTOPO ) # ntopo ) # neighbor
|
||||
FindStyleHeaders(${search_path} PAIR_CLASS pair_ PAIR ) # pair ) # force
|
||||
FindStyleHeaders(${search_path} READER_CLASS reader_ READER ) # reader ) # read_dump
|
||||
FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain
|
||||
endfunction(RegisterStyles)
|
||||
|
||||
function(RegisterStylesExt search_path extension sources)
|
||||
FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources})
|
||||
FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources})
|
||||
FindStyleHeadersExt(${search_path} BODY_CLASS ${extension} BODY ${sources})
|
||||
FindStyleHeadersExt(${search_path} BOND_CLASS ${extension} BOND ${sources})
|
||||
FindStyleHeadersExt(${search_path} COMMAND_CLASS ${extension} COMMAND ${sources})
|
||||
FindStyleHeadersExt(${search_path} COMPUTE_CLASS ${extension} COMPUTE ${sources})
|
||||
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
|
||||
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
|
||||
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
|
||||
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
|
||||
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
|
||||
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
|
||||
FindStyleHeadersExt(${search_path} MINIMIZE_CLASS ${extension} MINIMIZE ${sources})
|
||||
FindStyleHeadersExt(${search_path} NBIN_CLASS ${extension} NBIN ${sources})
|
||||
FindStyleHeadersExt(${search_path} NPAIR_CLASS ${extension} NPAIR ${sources})
|
||||
FindStyleHeadersExt(${search_path} NSTENCIL_CLASS ${extension} NSTENCIL ${sources})
|
||||
FindStyleHeadersExt(${search_path} NTOPO_CLASS ${extension} NTOPO ${sources})
|
||||
FindStyleHeadersExt(${search_path} PAIR_CLASS ${extension} PAIR ${sources})
|
||||
FindStyleHeadersExt(${search_path} READER_CLASS ${extension} READER ${sources})
|
||||
FindStyleHeadersExt(${search_path} REGION_CLASS ${extension} REGION ${sources})
|
||||
endfunction(RegisterStylesExt)
|
||||
|
||||
function(GenerateStyleHeaders output_path)
|
||||
GenerateStyleHeader(${output_path} ANGLE angle ) # force
|
||||
GenerateStyleHeader(${output_path} ATOM_VEC atom ) # atom atom_vec_hybrid
|
||||
GenerateStyleHeader(${output_path} BODY body ) # atom_vec_body
|
||||
GenerateStyleHeader(${output_path} BOND bond ) # force
|
||||
GenerateStyleHeader(${output_path} COMMAND command ) # input
|
||||
GenerateStyleHeader(${output_path} COMPUTE compute ) # modify
|
||||
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
|
||||
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
|
||||
GenerateStyleHeader(${output_path} FIX fix ) # modify
|
||||
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
|
||||
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
|
||||
GenerateStyleHeader(${output_path} KSPACE kspace ) # force
|
||||
GenerateStyleHeader(${output_path} MINIMIZE minimize ) # update
|
||||
GenerateStyleHeader(${output_path} NBIN nbin ) # neighbor
|
||||
GenerateStyleHeader(${output_path} NPAIR npair ) # neighbor
|
||||
GenerateStyleHeader(${output_path} NSTENCIL nstencil ) # neighbor
|
||||
GenerateStyleHeader(${output_path} NTOPO ntopo ) # neighbor
|
||||
GenerateStyleHeader(${output_path} PAIR pair ) # force
|
||||
GenerateStyleHeader(${output_path} READER reader ) # read_dump
|
||||
GenerateStyleHeader(${output_path} REGION region ) # domain
|
||||
endfunction(GenerateStyleHeaders)
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
cmake-buildsystem
|
||||
-----------------
|
||||
|
||||
To use the cmake build system instead of the make-driven one, do:
|
||||
```
|
||||
cmake /path/to/lammps/source/cmake
|
||||
```
|
||||
(please note the cmake directory as the very end)
|
||||
|
||||
To enable package, e.g. GPU do
|
||||
```
|
||||
cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON
|
||||
```
|
||||
|
||||
cmake has many many options, do get an overview use the curses-based cmake interface, ccmake:
|
||||
```
|
||||
ccmake /path/to/lammps/source/cmake
|
||||
```
|
||||
(Don't forget to press "g" for generate once you are done with configuring)
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
#define grdtyp double
|
||||
#define grdtyp4 double4
|
||||
|
||||
#include "lal_pppm.cu"
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
#define grdtyp float
|
||||
#define grdtyp4 float4
|
||||
|
||||
#include "lal_pppm.cu"
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 26 KiB |
|
|
@ -0,0 +1,21 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t),
|
||||
$$
|
||||
|
||||
$$
|
||||
r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}),
|
||||
$$
|
||||
|
||||
$$
|
||||
a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right],
|
||||
$$
|
||||
|
||||
$$
|
||||
v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t+\Delta t)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 32 KiB |
|
|
@ -0,0 +1,33 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{C} = \alpha_{ij}{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\omega_{C}(r) = 1 - r/r_c,
|
||||
$$
|
||||
|
||||
$$
|
||||
\alpha_{ij} = A\cdot k_B(T_i + T_j)/2,
|
||||
$$
|
||||
|
||||
$$
|
||||
\omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^s,
|
||||
$$
|
||||
|
||||
$$
|
||||
\sigma_{ij}^2 = 4\gamma k_B T_i T_j/(T_i + T_j),
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 17 KiB |
|
|
@ -0,0 +1,15 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2}=
|
||||
\frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}
|
||||
=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
|
||||
$$
|
||||
|
||||
$$
|
||||
C_v\frac{\mathrm{d} T_i}{\mathrm{d} t}= q_{i} = \sum_{i\neq j}(q_{ij}^{C}+q_{ij}^{V}+q_{ij}^{R}),
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 46 KiB |
|
|
@ -0,0 +1,29 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
q_i^C = \sum_{j \ne i} k_{ij} \omega_{CT}(r_{ij}) \left( \frac{1}{T_i} - \frac{1}{T_j} \right),
|
||||
$$
|
||||
|
||||
$$
|
||||
q_i^V = \frac{1}{2 C_v}\sum_{j \ne i}{ \left\{ \omega_D(r_{ij})\left[\gamma_{ij} \left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right)^2 - \frac{\left( \sigma _{ij} \right)^2}{m}\right] - \sigma _{ij} \omega_R(r_{ij})\left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right){\xi_{ij}} \right\} },
|
||||
$$
|
||||
|
||||
$$
|
||||
q_i^R = \sum_{j \ne i} \beta _{ij} \omega_{RT}(r_{ij}) d {t^{ - 1/2}} \xi_{ij}^e,
|
||||
$$
|
||||
|
||||
$$
|
||||
\omega_{CT}(r)=\omega_{RT}^2(r)=\left(1-r/r_{ct}\right)^{s_T},
|
||||
$$
|
||||
|
||||
$$
|
||||
k_{ij}=C_v^2\kappa(T_i + T_j)^2/4k_B,
|
||||
$$
|
||||
|
||||
$$
|
||||
\beta_{ij}^2=2k_Bk_{ij},
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 5.5 KiB |
|
|
@ -0,0 +1,9 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\kappa = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr},
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 19 KiB |
|
|
@ -0,0 +1,17 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^C = Aw_c(r_{ij})\mathbf{e}_{ij} + B(\rho_i+\rho_j)w_d(r_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 22 KiB |
|
|
@ -0,0 +1,21 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
Q_{ij}^D = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right),
|
||||
$$
|
||||
|
||||
$$
|
||||
Q_{ij}^R = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
w_{DC}(r_{ij})=w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}},
|
||||
$$
|
||||
|
||||
$$
|
||||
\epsilon_{ij}^2 = m_s^2\kappa_{ij}\rho,
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 25 KiB |
|
|
@ -0,0 +1,29 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{C} = A{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
|
||||
$$
|
||||
|
||||
$$
|
||||
\omega_{C}(r) = 1 - r/r_c,
|
||||
$$
|
||||
|
||||
$$
|
||||
\omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f},
|
||||
$$
|
||||
|
||||
$$
|
||||
\sigma^2 = 2\gamma k_B T,
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
|
|
@ -0,0 +1,13 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2} = \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
|
||||
$$
|
||||
|
||||
$$
|
||||
\frac{\mathrm{d} C_{i}}{\mathrm{d} t}= Q_{i} = \sum_{i\neq j}(Q_{ij}^{D}+Q_{ij}^{R}) + Q_{i}^{S},
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
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|
After Width: | Height: | Size: 895 KiB |
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|
After Width: | Height: | Size: 113 KiB |
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|
After Width: | Height: | Size: 38 KiB |
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|
After Width: | Height: | Size: 10 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 14 KiB After Width: | Height: | Size: 20 KiB |
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="11 Aug 2017 version">
|
||||
<META NAME="docnumber" CONTENT="1 Sep 2017 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 @@
|
|||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
11 Aug 2017 version :c,h4
|
||||
1 Sep 2017 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
|
@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
|
|||
"LAMMPS project on GitHub."_https://github.com/lammps/lammps
|
||||
The lammps.org domain, currently hosting "public continuous integration
|
||||
testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
|
||||
RPM and Windows installer packages"_http://rpm.lammps.org is located
|
||||
RPM and Windows installer packages"_http://packages.lammps.org is located
|
||||
at Temple University and managed by Richard Berger,
|
||||
richard.berger at temple.edu.
|
||||
|
||||
|
|
|
|||
Binary file not shown.
Binary file not shown.
|
|
@ -532,7 +532,8 @@ package"_Section_start.html#start_3.
|
|||
"dump vtk"_dump_vtk.html,
|
||||
"group2ndx"_group2ndx.html,
|
||||
"ndx2group"_group2ndx.html,
|
||||
"temper/grem"_temper_grem.html :tb(c=3,ea=c)
|
||||
"temper/grem"_temper_grem.html
|
||||
"temper/npt"_temper_npt.html :tb(c=3,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -685,6 +686,7 @@ package"_Section_start.html#start_3.
|
|||
"drude"_fix_drude.html,
|
||||
"drude/transform/direct"_fix_drude_transform.html,
|
||||
"drude/transform/reverse"_fix_drude_transform.html,
|
||||
"edpd/source"_fix_dpd_source.html,
|
||||
"eos/cv"_fix_eos_cv.html,
|
||||
"eos/table"_fix_eos_table.html,
|
||||
"eos/table/rx"_fix_eos_table_rx.html,
|
||||
|
|
@ -704,6 +706,9 @@ package"_Section_start.html#start_3.
|
|||
"meso"_fix_meso.html,
|
||||
"manifoldforce"_fix_manifoldforce.html,
|
||||
"meso/stationary"_fix_meso_stationary.html,
|
||||
"mvv/dpd"_fix_mvv_dpd.html,
|
||||
"mvv/edpd"_fix_mvv_dpd.html,
|
||||
"mvv/tdpd"_fix_mvv_dpd.html,
|
||||
"nve/dot"_fix_nve_dot.html,
|
||||
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
|
||||
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
|
||||
|
|
@ -732,6 +737,7 @@ package"_Section_start.html#start_3.
|
|||
"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
|
||||
"smd/setvel"_fix_smd_setvel.html,
|
||||
"smd/wall/surface"_fix_smd_wall_surface.html,
|
||||
"tdpd/source"_fix_dpd_source.html,
|
||||
"temp/rescale/eff"_fix_temp_rescale_eff.html,
|
||||
"ti/spring"_fix_ti_spring.html,
|
||||
"ttm/mod"_fix_ttm.html,
|
||||
|
|
@ -750,6 +756,7 @@ package"_Section_accelerate.html. This is indicated by additional
|
|||
letters in parenthesis: g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"aggregate/atom"_compute_cluster_atom.html,
|
||||
"angle"_compute_angle.html,
|
||||
"angle/local"_compute_angle_local.html,
|
||||
"angmom/chunk"_compute_angmom_chunk.html,
|
||||
|
|
@ -775,6 +782,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"erotate/sphere"_compute_erotate_sphere.html,
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
|
||||
"event/displace"_compute_event_displace.html,
|
||||
"fragment/atom"_compute_cluster_atom.html,
|
||||
"global/atom"_compute_global_atom.html,
|
||||
"group/group"_compute_group_group.html,
|
||||
"gyration"_compute_gyration.html,
|
||||
|
|
@ -836,6 +844,7 @@ package"_Section_start.html#start_3.
|
|||
"cnp/atom"_compute_cnp_atom.html,
|
||||
"dpd"_compute_dpd.html,
|
||||
"dpd/atom"_compute_dpd_atom.html,
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html,
|
||||
"fep"_compute_fep.html,
|
||||
"force/tally"_compute_tally.html,
|
||||
"heat/flux/tally"_compute_tally.html,
|
||||
|
|
@ -868,6 +877,7 @@ package"_Section_start.html#start_3.
|
|||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
|
||||
"smd/vol"_compute_smd_vol.html,
|
||||
"stress/tally"_compute_tally.html,
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
|
||||
"temp/drude"_compute_temp_drude.html,
|
||||
"temp/eff"_compute_temp_eff.html,
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html,
|
||||
|
|
@ -892,8 +902,8 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"hybrid"_pair_hybrid.html,
|
||||
"hybrid/overlay"_pair_hybrid.html,
|
||||
"adp (o)"_pair_adp.html,
|
||||
"airebo (o)"_pair_airebo.html,
|
||||
"airebo/morse (o)"_pair_airebo.html,
|
||||
"airebo (oi)"_pair_airebo.html,
|
||||
"airebo/morse (oi)"_pair_airebo.html,
|
||||
"beck (go)"_pair_beck.html,
|
||||
"body"_pair_body.html,
|
||||
"bop"_pair_bop.html,
|
||||
|
|
@ -927,8 +937,8 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"dpd/tstat (go)"_pair_dpd.html,
|
||||
"dsmc"_pair_dsmc.html,
|
||||
"eam (gkiot)"_pair_eam.html,
|
||||
"eam/alloy (gkot)"_pair_eam.html,
|
||||
"eam/fs (gkot)"_pair_eam.html,
|
||||
"eam/alloy (gkiot)"_pair_eam.html,
|
||||
"eam/fs (gkiot)"_pair_eam.html,
|
||||
"eim (o)"_pair_eim.html,
|
||||
"gauss (go)"_pair_gauss.html,
|
||||
"gayberne (gio)"_pair_gayberne.html,
|
||||
|
|
@ -942,9 +952,9 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"kim"_pair_kim.html,
|
||||
"lcbop"_pair_lcbop.html,
|
||||
"line/lj"_pair_line_lj.html,
|
||||
"lj/charmm/coul/charmm (ko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
|
||||
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long (giko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long (gkio)"_pair_charmm.html,
|
||||
"lj/charmm/coul/msm"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/long"_pair_charmm.html,
|
||||
|
|
@ -990,7 +1000,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"reax"_pair_reax.html,
|
||||
"rebo (o)"_pair_airebo.html,
|
||||
"rebo (oi)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
"snap"_pair_snap.html,
|
||||
"soft (go)"_pair_soft.html,
|
||||
|
|
@ -1024,6 +1034,7 @@ package"_Section_start.html#start_3.
|
|||
"eam/cd (o)"_pair_eam.html,
|
||||
"edip (o)"_pair_edip.html,
|
||||
"edip/multi"_pair_edip.html,
|
||||
"edpd"_pair_meso.html,
|
||||
"eff/cut"_pair_eff.html,
|
||||
"exp6/rx"_pair_exp6_rx.html,
|
||||
"gauss/cut"_pair_gauss.html,
|
||||
|
|
@ -1041,6 +1052,8 @@ package"_Section_start.html#start_3.
|
|||
"lj/sdk (gko)"_pair_sdk.html,
|
||||
"lj/sdk/coul/long (go)"_pair_sdk.html,
|
||||
"lj/sdk/coul/msm (o)"_pair_sdk.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
|
|
@ -1074,6 +1087,7 @@ package"_Section_start.html#start_3.
|
|||
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
|
||||
"srp"_pair_srp.html,
|
||||
"table/rx"_pair_table_rx.html,
|
||||
"tdpd"_pair_meso.html,
|
||||
"tersoff/table (o)"_pair_tersoff.html,
|
||||
"thole"_pair_thole.html,
|
||||
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
|
||||
|
|
|
|||
|
|
@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd
|
|||
|
||||
{New bond exceeded special list size in fix bond/create} :dt
|
||||
|
||||
See the "special_bonds extra" command
|
||||
(or the "read_data extra/special/per/atom" command)
|
||||
See the "read_data extra/special/per/atom" command
|
||||
(or the "create_box extra/special/per/atom" command)
|
||||
for info on how to leave space in the special bonds
|
||||
list to allow for additional bonds to be formed. :dd
|
||||
|
||||
|
|
@ -9666,8 +9666,8 @@ you are running. :dd
|
|||
|
||||
{Special list size exceeded in fix bond/create} :dt
|
||||
|
||||
See the special_bonds extra command
|
||||
(or the read_data extra/special/per/atom command)
|
||||
See the "read_data extra/special/per/atom" command
|
||||
(or the "create_box extra/special/per/atom" command)
|
||||
for info on how to leave space in the special bonds
|
||||
list to allow for additional bonds to be formed. :dd
|
||||
|
||||
|
|
|
|||
|
|
@ -2859,8 +2859,8 @@ The nature of the atoms (core, Drude particle or non-polarizable) is
|
|||
specified via the "fix drude"_fix_drude.html command. The special
|
||||
list of neighbors is automatically refactored to account for the
|
||||
equivalence of core and Drude particles as regards special 1-2 to 1-4
|
||||
screening. It may be necessary to use the {extra} keyword of the
|
||||
"special_bonds"_special_bonds.html command. If using "fix
|
||||
screening. It may be necessary to use the {extra/special/per/atom}
|
||||
keyword of the "read_data"_read_data.html command. If using "fix
|
||||
shake"_fix_shake.html, make sure no Drude particle is in this fix
|
||||
group.
|
||||
|
||||
|
|
|
|||
|
|
@ -112,7 +112,7 @@ Package, Description, Doc page, Example, Library
|
|||
"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
|
||||
"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
|
||||
"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
|
||||
"SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, -
|
||||
"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
|
||||
"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
|
||||
"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
|
||||
|
||||
|
|
@ -134,6 +134,7 @@ Package, Description, Doc page, Example, Library
|
|||
"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
|
||||
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
|
||||
"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
|
||||
"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
|
||||
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
|
||||
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
|
||||
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
|
||||
|
|
@ -1342,7 +1343,7 @@ make machine :pre
|
|||
[Supporting info:]
|
||||
|
||||
src/SNAP: filenames -> commands
|
||||
"pair snap"_pair_snap.html
|
||||
"pair_style snap"_pair_snap.html
|
||||
"compute sna/atom"_compute_sna_atom.html
|
||||
"compute snad/atom"_compute_sna_atom.html
|
||||
"compute snav/atom"_compute_sna_atom.html
|
||||
|
|
@ -1556,7 +1557,7 @@ make machine :pre
|
|||
|
||||
src/USER-AWPMD: filenames -> commands
|
||||
src/USER-AWPMD/README
|
||||
"pair awpmd/cut"_pair_awpmd.html
|
||||
"pair_style awpmd/cut"_pair_awpmd.html
|
||||
examples/USER/awpmd :ul
|
||||
|
||||
:line
|
||||
|
|
@ -1745,12 +1746,12 @@ src/USER-DPD: filenames -> commands
|
|||
"fix eos/table/rx"_fix_eos_table_rx.html
|
||||
"fix shardlow"_fix_shardlow.html
|
||||
"fix rx"_fix_rx.html
|
||||
"pair table/rx"_pair_table_rx.html
|
||||
"pair dpd/fdt"_pair_dpd_fdt.html
|
||||
"pair dpd/fdt/energy"_pair_dpd_fdt.html
|
||||
"pair exp6/rx"_pair_exp6_rx.html
|
||||
"pair multi/lucy"_pair_multi_lucy.html
|
||||
"pair multi/lucy/rx"_pair_multi_lucy_rx.html
|
||||
"pair_style table/rx"_pair_table_rx.html
|
||||
"pair_style dpd/fdt"_pair_dpd_fdt.html
|
||||
"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
|
||||
"pair_style exp6/rx"_pair_exp6_rx.html
|
||||
"pair_style multi/lucy"_pair_multi_lucy.html
|
||||
"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
|
||||
examples/USER/dpd :ul
|
||||
|
||||
:line
|
||||
|
|
@ -1785,8 +1786,8 @@ src/USER-DRUDE/README
|
|||
"fix drude"_fix_drude.html
|
||||
"fix drude/transform/*"_fix_drude_transform.html
|
||||
"compute temp/drude"_compute_temp_drude.html
|
||||
"pair thole"_pair_thole.html
|
||||
"pair lj/cut/thole/long"_pair_thole.html
|
||||
"pair_style thole"_pair_thole.html
|
||||
"pair_style lj/cut/thole/long"_pair_thole.html
|
||||
examples/USER/drude
|
||||
tools/drude :ul
|
||||
|
||||
|
|
@ -1824,8 +1825,8 @@ src/USER-EFF/README
|
|||
"fix npt/eff"_fix_nh_eff.html
|
||||
"fix langevin/eff"_fix_langevin_eff.html
|
||||
"compute temp/eff"_compute_temp_eff.html
|
||||
"pair eff/cut"_pair_eff.html
|
||||
"pair eff/inline"_pair_eff.html
|
||||
"pair_style eff/cut"_pair_eff.html
|
||||
"pair_style eff/inline"_pair_eff.html
|
||||
examples/USER/eff
|
||||
tools/eff/README
|
||||
tools/eff
|
||||
|
|
@ -2155,11 +2156,47 @@ make machine :pre
|
|||
|
||||
src/USER-MEAMC: filenames -> commands
|
||||
src/USER-MEAMC/README
|
||||
"pair meam/c"_pair_meam.html
|
||||
"pair_style meam/c"_pair_meam.html
|
||||
examples/meam :ul
|
||||
|
||||
:line
|
||||
|
||||
USER-MESO package :link(USER-MESO),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
Several extensions of the the dissipative particle dynamics (DPD)
|
||||
method. Specifically, energy-conserving DPD (eDPD) that can model
|
||||
non-isothermal processes, many-body DPD (mDPD) for simulating
|
||||
vapor-liquid coexistence, and transport DPD (tDPD) for modeling
|
||||
advection-diffuion-reaction systems. The equations of motion of these
|
||||
DPD extensions are integrated through a modified velocity-Verlet (MVV)
|
||||
algorithm.
|
||||
|
||||
[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
make yes-user-meso
|
||||
make machine :pre
|
||||
|
||||
make no-user-meso
|
||||
make machine :pre
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MESO: filenames -> commands
|
||||
src/USER-MESO/README
|
||||
"atom_style edpd"_atom_style.html
|
||||
"pair_style edpd"_pair_meso.html
|
||||
"pair_style mdpd"_pair_meso.html
|
||||
"pair_style tdpd"_pair_meso.html
|
||||
"fix mvv/dpd"_fix_mvv.html
|
||||
examples/USER/meso
|
||||
http://lammps.sandia.gov/movies.html#mesodpd :ul
|
||||
|
||||
:line
|
||||
|
||||
USER-MOLFILE package :link(USER-MOLFILE),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
|
|||
|
|
@ -536,7 +536,7 @@ You should get the executable lmp_foo when the build is complete.
|
|||
|
||||
:line
|
||||
|
||||
Errors that can occur when making LAMMPS: h5 :link(start_2_3)
|
||||
Errors that can occur when making LAMMPS :h5 :link(start_2_3)
|
||||
|
||||
If an error occurs when building LAMMPS, the compiler or linker will
|
||||
state very explicitly what the problem is. The error message should
|
||||
|
|
@ -662,27 +662,25 @@ your own build system. Due to differences between the Windows OS
|
|||
and Windows system libraries to Unix-like environments like Linux
|
||||
or MacOS, when compiling for Windows a few adjustments may be needed:
|
||||
|
||||
Do not set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
|
||||
Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
|
||||
Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
|
||||
Try adding -static-libgcc or -static or both to the linker flags when your
|
||||
LAMMPS executable complains about missing .dll files :ul
|
||||
Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul
|
||||
|
||||
Since none of the current LAMMPS core developers
|
||||
has significant experience building executables on Windows, we are
|
||||
happy to distribute contributed instructions and modifications, but
|
||||
we cannot provide support for those.
|
||||
Since none of the current LAMMPS core developers has significant
|
||||
experience building executables on Windows, we are happy to distribute
|
||||
contributed instructions and modifications to improve the situation,
|
||||
but we cannot provide support for those.
|
||||
|
||||
With the so-called "Anniversary Update" to Windows 10, there is a
|
||||
Ubuntu Linux subsystem available for Windows, that can be installed
|
||||
and then used to compile/install LAMMPS as if you are running on a
|
||||
Ubuntu Linux system instead of Windows.
|
||||
|
||||
As an alternative, you can download "daily builds" (and some older
|
||||
versions) of the installer packages from
|
||||
"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
|
||||
These executables are built with most optional packages and the
|
||||
download includes documentation, potential files, some tools and
|
||||
many examples, but no source code.
|
||||
As an alternative, you can download pre-compiled installer packages from
|
||||
"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
|
||||
These executables are built with most optional packages included and the
|
||||
download includes documentation, potential files, some tools and many
|
||||
examples, but no source code.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -1095,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages.
|
|||
:line
|
||||
|
||||
On a Windows box, you can skip making LAMMPS and simply download an
|
||||
installer package from "here"_http://rpm.lammps.org/windows.html
|
||||
installer package from "here"_http://packages.lammps.org/windows.html
|
||||
|
||||
For running the non-MPI executable, follow these steps:
|
||||
|
||||
|
|
@ -1107,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
|
|||
|
||||
At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
|
||||
with the name of your LAMMPS input script. :l
|
||||
|
||||
The serial executable includes support for multi-threading
|
||||
parallelization from the styles in the USER-OMP packages.
|
||||
|
||||
To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
|
||||
:ule
|
||||
|
||||
For the MPI version, which allows you to run LAMMPS under Windows on
|
||||
multiple processors, follow these steps:
|
||||
For the MPI version, which allows you to run LAMMPS under Windows with
|
||||
the more general message passing parallel library (LAMMPS has been
|
||||
designed from ground up to use MPI efficiently), follow these steps:
|
||||
|
||||
Download and install
|
||||
"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
|
||||
for Windows. :ulb,l
|
||||
Download and install a compatible MPI library binary package:
|
||||
for 32-bit Windows
|
||||
"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
|
||||
and for 64-bit Windows
|
||||
"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
|
||||
:ulb,l
|
||||
|
||||
The LAMMPS Windows installer packages will automatically adjust your
|
||||
path for the default location of this MPI package. After the installation
|
||||
of the MPICH software, it needs to be integrated into the system.
|
||||
of the MPICH2 software, it needs to be integrated into the system.
|
||||
For this you need to start a Command Prompt in {Administrator Mode}
|
||||
(right click on the icon and select it). Change into the MPICH2
|
||||
installation directory, then into the subdirectory [bin] and execute
|
||||
|
|
@ -1137,7 +1144,7 @@ or
|
|||
|
||||
mpiexec -np 4 lmp_mpi -in in.lj :pre
|
||||
|
||||
replacing in.lj with the name of your LAMMPS input script. For the latter
|
||||
replacing [in.lj] with the name of your LAMMPS input script. For the latter
|
||||
case, you may be prompted to enter your password. :l
|
||||
|
||||
In this mode, output may not immediately show up on the screen, so if
|
||||
|
|
@ -1149,6 +1156,11 @@ something like:
|
|||
|
||||
lmp_mpi -in in.lj :pre
|
||||
|
||||
And the parallel executable also includes OpenMP multi-threading, which
|
||||
can be combined with MPI using something like:
|
||||
|
||||
mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
|
||||
|
||||
:ule
|
||||
|
||||
:line
|
||||
|
|
|
|||
|
|
@ -29,8 +29,10 @@ Bond Styles: fene, harmonic :l
|
|||
Dihedral Styles: charmm, harmonic, opls :l
|
||||
Fixes: nve, npt, nvt, nvt/sllod :l
|
||||
Improper Styles: cvff, harmonic :l
|
||||
Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
|
||||
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
|
||||
buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
|
||||
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
|
||||
sw, tersoff :l
|
||||
K-Space Styles: pppm, pppm/disp :l
|
||||
:ule
|
||||
|
||||
|
|
|
|||
|
|
@ -13,15 +13,17 @@ atom_style command :h3
|
|||
atom_style style args :pre
|
||||
|
||||
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
|
||||
{dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
|
||||
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
|
||||
{template} or {hybrid} :ulb,l
|
||||
{dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
|
||||
{full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
|
||||
{sphere} or {tri} or {template} or {hybrid} :ulb,l
|
||||
args = none for any style except the following
|
||||
{body} args = bstyle bstyle-args
|
||||
bstyle = style of body particles
|
||||
bstyle-args = additional arguments specific to the bstyle
|
||||
see the "body"_body.html doc page for details
|
||||
{template} args = template-ID
|
||||
{tdpd} arg = Nspecies
|
||||
Nspecies = # of chemical species
|
||||
{template} arg = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{hybrid} args = list of one or more sub-styles, each with their args :pre
|
||||
|
||||
|
|
@ -36,7 +38,8 @@ atom_style full
|
|||
atom_style body nparticle 2 10
|
||||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5
|
||||
atom_style template myMols :pre
|
||||
atom_style template myMols
|
||||
atom_style tdpd 2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -74,6 +77,9 @@ quantities.
|
|||
{charge} | charge | atomic system with charges |
|
||||
{dipole} | charge and dipole moment | system with dipolar particles |
|
||||
{dpd} | internal temperature and internal energies | DPD particles |
|
||||
{edpd} | temperature and heat capacity | eDPD particles |
|
||||
{mdpd} | density | mDPD particles |
|
||||
{tdpd} | chemical concentration | tDPD particles |
|
||||
{electron} | charge and spin and eradius | electronic force field |
|
||||
{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
|
||||
{full} | molecular + charge | bio-molecules |
|
||||
|
|
@ -145,6 +151,19 @@ properties with internal temperature (dpdTheta), internal conductive
|
|||
energy (uCond), internal mechanical energy (uMech), and internal
|
||||
chemical energy (uChem).
|
||||
|
||||
The {edpd} style is for energy-conserving dissipative particle
|
||||
dynamics (eDPD) particles which store a temperature (edpd_temp), and
|
||||
heat capacity(edpd_cv).
|
||||
|
||||
The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
|
||||
particles which store a density (rho) for considering
|
||||
density-dependent many-body interactions.
|
||||
|
||||
The {tdpd} style is for transport dissipative particle dynamics (tDPD)
|
||||
particles which store a set of chemical concentration. An integer
|
||||
"cc_species" is required to specify the number of chemical species
|
||||
involved in a tDPD system.
|
||||
|
||||
The {meso} style is for smoothed particle hydrodynamics (SPH)
|
||||
particles which store a density (rho), energy (e), and heat capacity
|
||||
(cv).
|
||||
|
|
@ -284,6 +303,11 @@ force fields"_pair_eff.html.
|
|||
The {dpd} style is part of the USER-DPD package for dissipative
|
||||
particle dynamics (DPD).
|
||||
|
||||
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
|
||||
for energy-conserving dissipative particle dynamics (eDPD), many-body
|
||||
dissipative particle dynamics (mDPD), and transport dissipative particle
|
||||
dynamics (tDPD), respectively.
|
||||
|
||||
The {meso} style is part of the USER-SPH package for smoothed particle
|
||||
hydrodynamics (SPH). See "this PDF
|
||||
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ Commands :h1
|
|||
tad
|
||||
temper
|
||||
temper_grem
|
||||
temper_npt
|
||||
thermo
|
||||
thermo_modify
|
||||
thermo_style
|
||||
|
|
|
|||
|
|
@ -169,6 +169,7 @@ by users which are included in the LAMMPS distribution. The list of
|
|||
these with links to the individual styles are given in the compute
|
||||
section of "this page"_Section_commands.html#cmd_5.
|
||||
|
||||
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
|
||||
"angle/local"_compute_bond_local.html - theta and energy of each angle
|
||||
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
|
||||
"body/local"_compute_body_local.html - attributes of body sub-particles
|
||||
|
|
@ -191,6 +192,7 @@ section of "this page"_Section_commands.html#cmd_5.
|
|||
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
||||
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
|
||||
"event/displace"_compute_event_displace.html - detect event on atom displacement
|
||||
"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
|
||||
"group/group"_compute_group_group.html - energy/force between two groups of atoms
|
||||
"gyration"_compute_gyration.html - radius of gyration of group of atoms
|
||||
"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
|
||||
|
|
|
|||
|
|
@ -7,37 +7,62 @@
|
|||
:line
|
||||
|
||||
compute cluster/atom command :h3
|
||||
compute fragment/atom command :h3
|
||||
compute aggregate/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID cluster/atom cutoff :pre
|
||||
compute ID group-ID cluster/atom cutoff
|
||||
compute ID group-ID fragment/atom
|
||||
compute ID group-ID aggregate/atom cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
cluster/atom = style name of this compute command
|
||||
{cluster/atom} or {fragment/atom} or {aggregate/atom} = style name of this compute command
|
||||
cutoff = distance within which to label atoms as part of same cluster (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all cluster/atom 1.0 :pre
|
||||
compute 1 all cluster/atom 3.5
|
||||
compute 1 all fragment/atom :pre
|
||||
compute 1 all aggregate/atom 3.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that assigns each atom a cluster ID.
|
||||
Define a computation that assigns each atom a cluster, fragement,
|
||||
or aggregate ID.
|
||||
|
||||
A cluster is defined as a set of atoms, each of which is within the
|
||||
cutoff distance from one or more other atoms in the cluster. If an
|
||||
atom has no neighbors within the cutoff distance, then it is a 1-atom
|
||||
cluster. The ID of every atom in the cluster will be the smallest
|
||||
atom ID of any atom in the cluster.
|
||||
cluster.
|
||||
|
||||
A fragment is similarly defined as a set of atoms, each of
|
||||
which has an explicit bond (i.e. defined via a "data file"_read_data.html,
|
||||
the "create_bonds"_create_bonds.html command, or through fixes like
|
||||
"fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
|
||||
or "fix bond/break"_fix_bond_break.html). The cluster ID or fragment ID
|
||||
of every atom in the cluster will be set to the smallest atom ID of any atom
|
||||
in the cluster or fragment, respectively.
|
||||
|
||||
An aggregate is defined by combining the rules for clusters and
|
||||
fragments, i.e. a set of atoms, where each of it is within the cutoff
|
||||
distance from one or more atoms within a fragment that is part of
|
||||
the same cluster. This measure can be used to track molecular assemblies
|
||||
like micelles.
|
||||
|
||||
Only atoms in the compute group are clustered and assigned cluster
|
||||
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
|
||||
For fragments, only bonds where [both] atoms of the bond are included
|
||||
in the compute group are assigned to fragments, so that only fragmets
|
||||
are detected where [all] atoms are in the compute group. Thus atoms
|
||||
may be included in the compute group, yes still have a fragment ID of 0.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. 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 of a
|
||||
{cluster/atom} style.
|
||||
For computes {cluster/atom} and {aggregate/atom} the neighbor list needed
|
||||
to compute this quantity is constructed each time the calculation is
|
||||
performed (i.e. 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 of a {cluster/atom} or
|
||||
{aggregate/atom} style.
|
||||
|
||||
NOTE: If you have a bonded system, then the settings of
|
||||
"special_bonds"_special_bonds.html command can remove pairwise
|
||||
|
|
|
|||
|
|
@ -0,0 +1,62 @@
|
|||
"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 edpd/temp/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID edpd/temp/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
edpd/temp/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all edpd/temp/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the per-atom temperature
|
||||
for each eDPD particle in a group.
|
||||
|
||||
The temperature is a local temperature derived from the internal energy
|
||||
of each eDPD particle based on the local equilibrium hypothesis.
|
||||
For more details please see "(Espanol1997)"_#Espanol1997 and
|
||||
"(Li2014)"_#Li2014a.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a per-atom vector, 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.
|
||||
|
||||
The per-atom vector values will be in temperature "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-MESO package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style edpd"_pair_meso.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Espanol1997)
|
||||
[(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:
|
||||
10.1209/epl/i1997-00515-8
|
||||
|
||||
:link(Li2014a)
|
||||
[(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265:
|
||||
113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.
|
||||
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
"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 tdpd/cc/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID tdpd/cc/atom index :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
tdpd/cc/atom = style name of this compute command
|
||||
index = index of chemical species (1 to Nspecies) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all tdpd/cc/atom 2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the per-atom chemical
|
||||
concentration of a specified species for each tDPD particle in a
|
||||
group.
|
||||
|
||||
The chemical concentration of each species is defined as the number of
|
||||
molecules carried by a tDPD particle for dilute solution. For more
|
||||
details see "(Li2015)"_#Li2015a.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a per-atom vector, 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.
|
||||
|
||||
The per-atom vector values will be in the units of chemical species
|
||||
per unit mass.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-MESO package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style tdpd"_pair_meso.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Li2015a)
|
||||
[(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143:
|
||||
014101 (2015). DOI: 10.1063/1.4923254
|
||||
|
||||
|
|
@ -30,6 +30,7 @@ Computes :h1
|
|||
compute_displace_atom
|
||||
compute_dpd
|
||||
compute_dpd_atom
|
||||
compute_edpd_temp_atom
|
||||
compute_erotate_asphere
|
||||
compute_erotate_rigid
|
||||
compute_erotate_sphere
|
||||
|
|
@ -95,6 +96,7 @@ Computes :h1
|
|||
compute_sna_atom
|
||||
compute_stress_atom
|
||||
compute_tally
|
||||
compute_tdpd_cc_atom
|
||||
compute_temp
|
||||
compute_temp_asphere
|
||||
compute_temp_body
|
||||
|
|
|
|||
|
|
@ -150,10 +150,9 @@ atoms. Note that adding a single bond always adds a new 1st neighbor
|
|||
but may also induce *many* new 2nd and 3rd neighbors, depending on the
|
||||
molecular topology of your system. The "extra special per atom"
|
||||
parameter must typically be set to allow for the new maximum total
|
||||
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
|
||||
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2
|
||||
ways to do this. See the "read_data"_read_data.html or
|
||||
"create_box"_create_box.html or "special_bonds extra" commands for
|
||||
details.
|
||||
"create_box"_create_box.html commands for details.
|
||||
|
||||
NOTE: Even if you do not use the {atype}, {dtype}, or {itype}
|
||||
keywords, the list of topological neighbors is updated for atoms
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
fix dpd/energy command :h3
|
||||
fix dpd/energy/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -46,6 +47,29 @@ examples/USER/dpd directory.
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -0,0 +1,101 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix edpd/source command :h3
|
||||
fix tdpd/source command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID edpd/source keyword values ...
|
||||
fix ID group-ID tdpd/source cc_index keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
edpd/source or tdpd/source = style name of this fix command :l
|
||||
index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) :l
|
||||
keyword = {sphere} or {cuboid} :l
|
||||
{sphere} values = cx,cy,cz,radius,source
|
||||
cx,cy,cz = x,y,z center of spherical domain (distance units)
|
||||
radius = radius of a spherical domain (distance units)
|
||||
source = heat source or concentration source (flux units, see below)
|
||||
{cuboid} values = cx,cy,cz,dLx,dLy,dLz,source
|
||||
cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units)
|
||||
dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
|
||||
source = heat source or concentration source (flux units, see below) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01
|
||||
fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
|
||||
fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
|
||||
fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Fix {edpd/source} adds a heat source as an external heat flux to each
|
||||
atom in a spherical or cuboid domain, where the {source} is in units
|
||||
of energy/time. Fix {tdpd/source} adds an external concentration
|
||||
source of the chemical species specified by {index} as an external
|
||||
concentration flux for each atom in a spherical or cuboid domain,
|
||||
where the {source} is in units of mole/volume/time.
|
||||
|
||||
This command can be used to give an additional heat/concentration
|
||||
source term to atoms in a simulation, such as for a simulation of a
|
||||
heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b)
|
||||
or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as
|
||||
an analog of a periodic Poiseuille flow problem.
|
||||
|
||||
If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a
|
||||
spherical domain to apply the source flux to.
|
||||
|
||||
If the {cuboid} keyword is used, the {cx,cy,cz,dLx,dLy,dLz} defines a
|
||||
cuboid domain to apply the source flux to.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MESO package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Fix {edpd/source} must be used with the "pair_style
|
||||
edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the
|
||||
"pair_style tdpd"_pair_meso.html command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style edpd"_pair_meso.html, "pair_style tdpd"_pair_meso.html,
|
||||
"compute edpd/temp/atom"_compute_edpd_temp_atom.html, "compute
|
||||
tdpd/cc/atom"_compute_tdpd_cc_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Li2014b)
|
||||
[(Li2014)] Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis,
|
||||
"Energy-conserving dissipative particle dynamics with
|
||||
temperature-dependent properties", J. Comput. Phys., 265: 113-127
|
||||
(2014). DOI: 10.1016/j.jcp.2014.02.003
|
||||
|
||||
:link(Li2015b)
|
||||
[(Li2015)] Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis,
|
||||
"Transport dissipative particle dynamics model for mesoscopic
|
||||
advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101
|
||||
(2015). DOI: 10.1063/1.4923254
|
||||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
fix eos/table/rx command :h3
|
||||
fix eos/table/rx/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -152,6 +153,29 @@ no 0.93 0.00 0.000 -1.76 :pre
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -0,0 +1,97 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix mvv/dpd command :h3
|
||||
fix mvv/edpd command :h3
|
||||
fix mvv/tdpd command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID mvv/dpd lambda :pre
|
||||
fix ID group-ID mvv/edpd lambda :pre
|
||||
fix ID group-ID mvv/tdpd lambda :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
mvv/dpd, mvv/edpd, mvv/tdpd = style name of this fix command
|
||||
lambda = (optional) relaxation parameter (unitless) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all mvv/dpd
|
||||
fix 1 all mvv/dpd 0.5
|
||||
fix 1 all mvv/edpd
|
||||
fix 1 all mvv/edpd 0.5
|
||||
fix 1 all mvv/tdpd
|
||||
fix 1 all mvv/tdpd 0.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform time integration using the modified velocity-Verlet (MVV)
|
||||
algorithm to update position and velocity (fix mvv/dpd), or position,
|
||||
velocity and temperature (fix mvv/edpd), or position, velocity and
|
||||
concentration (fix mvv/tdpd) for particles in the group each timestep.
|
||||
|
||||
The modified velocity-Verlet (MVV) algorithm aims to improve the
|
||||
stability of the time integrator by using an extrapolated version of
|
||||
the velocity for the force evaluation:
|
||||
|
||||
:c,image(Eqs/fix_mvv_dpd.jpg)
|
||||
|
||||
where the parameter <font size="4">λ</font> depends on the
|
||||
specific choice of DPD parameters, and needs to be tuned on a
|
||||
case-by-case basis. Specification of a {lambda} value is opttional.
|
||||
If specified, the setting must be from 0.0 to 1.0. If not specified,
|
||||
a default value of 0.5 is used, which effectively reproduces the
|
||||
standard velocity-Verlet (VV) scheme. For more details, see
|
||||
"Groot"_#Groot2.
|
||||
|
||||
Fix {mvv/dpd} updates the position and velocity of each atom. It can
|
||||
be used with the "pair_style mdpd"_pair_meso.html command or other
|
||||
pair styles such as "pair dpd"_pair_dpd.html.
|
||||
|
||||
Fix {mvv/edpd} updates the per-atom temperature, in addition to
|
||||
position and velocity, and must be used with the "pair_style
|
||||
edpd"_pair_meso.html command.
|
||||
|
||||
Fix {mvv/tdpd} updates the per-atom chemical concentration, in
|
||||
addition to position and velocity, and must be used with the
|
||||
"pair_style tdpd"_pair_meso.html command.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MESO package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style mdpd"_pair_meso.html, "pair_style edpd"_pair_meso.html,
|
||||
"pair_style tdpd"_pair_meso.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default value for the optional {lambda} parameter is 0.5.
|
||||
|
||||
:line
|
||||
|
||||
:link(Groot2)
|
||||
[(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:
|
||||
10.1063/1.474784
|
||||
|
||||
|
|
@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
|
|||
[Restrictions:]
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
|
||||
"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -24,7 +24,8 @@ keyword = {angmom} :l
|
|||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
|
||||
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -78,7 +79,9 @@ a Gaussian random number) for speed.
|
|||
:line
|
||||
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
be variables.
|
||||
be variables. If used together with the oxDNA force field for
|
||||
coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
|
||||
corresponds to T = 300 K.
|
||||
|
||||
The {damp} parameter is specified in time units and determines how
|
||||
rapidly the temperature is relaxed. For example, a value of 0.03
|
||||
|
|
@ -89,6 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
|
|||
hi-viscosity solvent and vice versa. See the discussion about gamma
|
||||
and viscosity in the documentation for the "fix
|
||||
viscous"_fix_viscous.html command for more details.
|
||||
Note that the value 78.9375 in the second example above corresponds
|
||||
to a diffusion constant, which is about an order of magnitude larger
|
||||
than realistic ones. This has been used to sample configurations faster
|
||||
in Brownian dynamics simulations.
|
||||
|
||||
The random # {seed} must be a positive integer. A Marsaglia random
|
||||
number generator is used. Each processor uses the input seed to
|
||||
|
|
@ -115,12 +122,12 @@ A technical report with more information on this integrator can be found
|
|||
[Restrictions:]
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
|
||||
"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -90,9 +90,14 @@ file specified by {qfile}. The file has the following format
|
|||
...
|
||||
Ntype chi eta gamma zeta qcore :pre
|
||||
|
||||
There is one line per atom type with the following parameters.
|
||||
There have to be parameters given for every atom type. Wildcard entries
|
||||
are possible using the same syntax as elsewhere in LAMMPS
|
||||
(i.e., n*m, n*, *m, *). Later entries will overwrite previous ones.
|
||||
Empty lines or any text following the pound sign (#) are ignored.
|
||||
Each line starts with the atom type followed by five parameters.
|
||||
Only a subset of the parameters is used by each QEq style as described
|
||||
below, thus the others can be set to 0.0 if desired.
|
||||
below, thus the others can be set to 0.0 if desired, but all five
|
||||
entries per line are required.
|
||||
|
||||
{chi} = electronegativity in energy units
|
||||
{eta} = self-Coulomb potential in energy units
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
fix rx command :h3
|
||||
fix rx/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -182,6 +183,29 @@ read_data data.dpd fix foo_SPECIES NULL Species
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -37,8 +37,8 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l
|
|||
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
|
||||
|
||||
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
|
||||
fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
fix shardlow command :h3
|
||||
fix shardlow/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -52,6 +53,29 @@ examples/USER/dpd directory.
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
fix wall/lj93 command :h3
|
||||
fix wall/lj93/kk command :h3
|
||||
fix wall/lj126 command :h3
|
||||
fix wall/lj1043 command :h3
|
||||
fix wall/colloid command :h3
|
||||
|
|
@ -277,6 +278,31 @@ the total potential energy of the system (the quantity being
|
|||
minimized), you MUST enable the "fix_modify"_fix_modify.html {energy}
|
||||
option for this fix.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -50,17 +50,17 @@ fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre
|
|||
Fix {wall/ees} bounds the simulation domain on one or more of its
|
||||
faces with a flat wall that interacts with the ellipsoidal atoms in the
|
||||
group by generating a force on the atom in a direction perpendicular to
|
||||
the wall and a torque parallel with the wall. The energy of
|
||||
the wall and a torque parallel with the wall. The energy of
|
||||
wall-particle interactions E is given by:
|
||||
|
||||
:c,image(Eqs/fix_wall_ees.jpg)
|
||||
|
||||
Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here,
|
||||
{r} is the distance from the particle to the wall at position {coord},
|
||||
and Rc is the {cutoff} distance at which the particle and wall no
|
||||
longer interact. Also, sigma_n is the distance between center of
|
||||
ellipsoid and the nearest point of its surface to the wall The energy
|
||||
of the wall (see the image below).
|
||||
and Rc is the {cutoff} distance at which the particle and wall no
|
||||
longer interact. Also, sigma_n is the distance between center of
|
||||
ellipsoid and the nearest point of its surface to the wall. The energy
|
||||
of the wall is:
|
||||
|
||||
:c,image(JPG/fix_wall_ees_image.jpg)
|
||||
|
||||
|
|
@ -68,20 +68,21 @@ Details of using this command and specifications are the same as
|
|||
fix/wall command. You can also find an example in USER/ees/ under
|
||||
examples/ directory.
|
||||
|
||||
The prefactor {epsilon} can be thought of as an
|
||||
effective Hamaker constant with energy units for the strength of the
|
||||
ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor
|
||||
= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
|
||||
* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
|
||||
the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
|
||||
of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
|
||||
The prefactor {epsilon} can be thought of as an
|
||||
effective Hamaker constant with energy units for the strength of the
|
||||
ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor
|
||||
= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
|
||||
* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
|
||||
the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
|
||||
of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
|
||||
density of the constituent particles, in the wall and ellipsoid
|
||||
respectively, in units of 1/volume.
|
||||
|
||||
NOTE: You must insure that r is always bigger than sigma_n for
|
||||
all particles in the group, or LAMMPS will generate an error. This
|
||||
all particles in the group, or LAMMPS will generate an error. This
|
||||
means you cannot start your simulation with particles touching the wall
|
||||
position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the
|
||||
position {coord} (r = sigma_n) or with particles penetrating the wall
|
||||
(0 =< r < sigma_n) or with particles on the wrong side of the
|
||||
wall (r < 0).
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@ Fixes :h1
|
|||
fix_drude
|
||||
fix_drude_transform
|
||||
fix_dpd_energy
|
||||
fix_dpd_source
|
||||
fix_dt_reset
|
||||
fix_efield
|
||||
fix_ehex
|
||||
|
|
@ -71,6 +72,7 @@ Fixes :h1
|
|||
fix_move
|
||||
fix_mscg
|
||||
fix_msst
|
||||
fix_mvv_dpd
|
||||
fix_neb
|
||||
fix_nh
|
||||
fix_nh_eff
|
||||
|
|
|
|||
|
|
@ -21,6 +21,7 @@ Section_python.html
|
|||
Section_errors.html
|
||||
Section_history.html
|
||||
|
||||
tutorial_bash_on_windows.html
|
||||
tutorial_drude.html
|
||||
tutorial_github.html
|
||||
tutorial_pylammps.html
|
||||
|
|
@ -115,6 +116,7 @@ suffix.html
|
|||
tad.html
|
||||
temper.html
|
||||
temper_grem.html
|
||||
temper_npt.html
|
||||
thermo.html
|
||||
thermo_modify.html
|
||||
thermo_style.html
|
||||
|
|
@ -156,6 +158,7 @@ fix_controller.html
|
|||
fix_deform.html
|
||||
fix_deposit.html
|
||||
fix_dpd_energy.html
|
||||
fix_dpd_source.html
|
||||
fix_drag.html
|
||||
fix_drude.html
|
||||
fix_drude_transform.html
|
||||
|
|
@ -197,6 +200,7 @@ fix_momentum.html
|
|||
fix_move.html
|
||||
fix_mscg.html
|
||||
fix_msst.html
|
||||
fix_mvv_dpd.html
|
||||
fix_neb.html
|
||||
fix_nh.html
|
||||
fix_nh_eff.html
|
||||
|
|
@ -315,6 +319,7 @@ compute_dipole_chunk.html
|
|||
compute_displace_atom.html
|
||||
compute_dpd.html
|
||||
compute_dpd_atom.html
|
||||
compute_edpd_temp_atom.html
|
||||
compute_erotate_asphere.html
|
||||
compute_erotate_rigid.html
|
||||
compute_erotate_sphere.html
|
||||
|
|
@ -380,6 +385,7 @@ compute_smd_vol.html
|
|||
compute_sna_atom.html
|
||||
compute_stress_atom.html
|
||||
compute_tally.html
|
||||
compute_tdpd_cc_atom.html
|
||||
compute_temp.html
|
||||
compute_temp_asphere.html
|
||||
compute_temp_body.html
|
||||
|
|
@ -457,6 +463,7 @@ pair_mdf.html
|
|||
pair_meam.html
|
||||
pair_meam_spline.html
|
||||
pair_meam_sw_spline.html
|
||||
pair_meso.html
|
||||
pair_mgpt.html
|
||||
pair_mie.html
|
||||
pair_momb.html
|
||||
|
|
@ -644,4 +651,3 @@ USER/atc/man_unfix_flux.html
|
|||
USER/atc/man_unfix_nodes.html
|
||||
USER/atc/man_write_atom_weights.html
|
||||
USER/atc/man_write_restart.html
|
||||
|
||||
|
|
|
|||
|
|
@ -7,10 +7,13 @@
|
|||
:line
|
||||
|
||||
pair_style airebo command :h3
|
||||
pair_style airebo/intel command :h3
|
||||
pair_style airebo/omp command :h3
|
||||
pair_style airebo/morse command :h3
|
||||
pair_style airebo/morse/intel command :h3
|
||||
pair_style airebo/morse/omp command :h3
|
||||
pair_style rebo command :h3
|
||||
pair_style rebo/intel command :h3
|
||||
pair_style rebo/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
pair_style lj/charmm/coul/charmm command :h3
|
||||
pair_style lj/charmm/coul/charmm/intel command :h3
|
||||
pair_style lj/charmm/coul/charmm/omp command :h3
|
||||
pair_style lj/charmm/coul/charmm/implicit command :h3
|
||||
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ pair_coeff 1 1 1.0 1.0 :pre
|
|||
[Description:]
|
||||
|
||||
Style {dpd} computes a force field for dissipative particle dynamics
|
||||
(DPD) following the exposition in "(Groot)"_#Groot.
|
||||
(DPD) following the exposition in "(Groot)"_#Groot1.
|
||||
|
||||
Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
|
||||
which is equivalent to the non-conservative portion of the DPD force
|
||||
|
|
@ -196,7 +196,7 @@ langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html
|
|||
|
||||
:line
|
||||
|
||||
:link(Groot)
|
||||
:link(Groot1)
|
||||
[(Groot)] Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
||||
|
||||
:link(Afshar)
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@
|
|||
|
||||
pair_style dpd/fdt command :h3
|
||||
pair_style dpd/fdt/energy command :h3
|
||||
pair_style dpd/fdt/energy/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -125,6 +126,29 @@ significantly larger timesteps to be taken.
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These commands are part of the USER-DPD package. They are only
|
||||
|
|
|
|||
|
|
@ -14,6 +14,7 @@ pair_style eam/omp command :h3
|
|||
pair_style eam/opt command :h3
|
||||
pair_style eam/alloy command :h3
|
||||
pair_style eam/alloy/gpu command :h3
|
||||
pair_style eam/alloy/intel command :h3
|
||||
pair_style eam/alloy/kk command :h3
|
||||
pair_style eam/alloy/omp command :h3
|
||||
pair_style eam/alloy/opt command :h3
|
||||
|
|
@ -21,6 +22,7 @@ pair_style eam/cd command :h3
|
|||
pair_style eam/cd/omp command :h3
|
||||
pair_style eam/fs command :h3
|
||||
pair_style eam/fs/gpu command :h3
|
||||
pair_style eam/fs/intel command :h3
|
||||
pair_style eam/fs/kk command :h3
|
||||
pair_style eam/fs/omp command :h3
|
||||
pair_style eam/fs/opt command :h3
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
pair_style exp6/rx command :h3
|
||||
pair_style exp6/rx/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -147,6 +148,31 @@ This style does not support the pair_modify tail option for adding long-range
|
|||
tail corrections to energy and pressure for the A,C terms in the
|
||||
pair interaction.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ pair_style hybrid command :h3
|
|||
pair_style hybrid/omp command :h3
|
||||
pair_style hybrid/overlay command :h3
|
||||
pair_style hybrid/overlay/omp command :h3
|
||||
pair_style hybrid/overlay/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,277 @@
|
|||
"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
|
||||
|
||||
pair_style edpd command :h3
|
||||
pair_style mdpd command :h3
|
||||
pair_style mdpd/rhosum command :h3
|
||||
pair_style tdpd command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {edpd} or {mdpd} or {mdpd/rhosum} or {tdpd} :ulb,l
|
||||
args = list of arguments for a particular style :l
|
||||
{edpd} args = cutoff seed
|
||||
cutoff = global cutoff for eDPD interactions (distance units)
|
||||
seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed)
|
||||
{mdpd} args = T cutoff seed
|
||||
T = temperature (temperature units)
|
||||
cutoff = global cutoff for mDPD interactions (distance units)
|
||||
seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed)
|
||||
{mdpd/rhosum} args =
|
||||
{tdpd} args = T cutoff seed
|
||||
T = temperature (temperature units)
|
||||
cutoff = global cutoff for tDPD interactions (distance units)
|
||||
seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style edpd 1.58 9872598
|
||||
pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58
|
||||
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10
|
||||
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 :pre
|
||||
|
||||
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 65689
|
||||
pair_coeff 1 1 mdpd/rhosum 0.75
|
||||
pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre
|
||||
|
||||
pair_style tdpd 1.0 1.58 935662
|
||||
pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
|
||||
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {edpd} style computes the pairwise interactions and heat fluxes
|
||||
for eDPD particles following the formulations in
|
||||
"(Li2014_JCP)"_#Li2014_JCP and "Li2015_CC"_#Li2015_CC. The time
|
||||
evolution of an eDPD particle is governed by the conservation of
|
||||
momentum and energy given by
|
||||
|
||||
:c,image(Eqs/pair_edpd_gov.jpg)
|
||||
|
||||
where the three components of <font size="4">F<sub>i</sub></font>
|
||||
including the conservative force <font
|
||||
size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
|
||||
size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
|
||||
size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
|
||||
|
||||
:c,image(Eqs/pair_edpd_force.jpg)
|
||||
|
||||
in which the exponent of the weighting function <font
|
||||
size="4"><i>s</i></font> can be defined as a temperature-dependent
|
||||
variable. The heat flux between particles accounting for the
|
||||
collisional heat flux <font size="4">q<sup>C</sup></font>, viscous
|
||||
heat flux <font size="4">q<sup>V</sup></font>, and random heat flux
|
||||
<font size="4">q<sup>R</sup></font> are given by
|
||||
|
||||
:c,image(Eqs/pair_edpd_heat.jpg)
|
||||
|
||||
where the mesoscopic heat friction <font size="4">κ</font> is given by
|
||||
|
||||
:c,image(Eqs/pair_edpd_kappa.jpg)
|
||||
|
||||
with <font size="4">υ</font> being the kinematic
|
||||
viscosity. For more details, see Eq.(15) in "(Li2014_JCP)"_#Li2014_JCP.
|
||||
|
||||
The following coefficients must be defined in eDPD system for each
|
||||
pair of atom types via the "pair_coeff"_pair_coeff.html command as in
|
||||
the examples above.
|
||||
|
||||
A (force units)
|
||||
gamma (force/velocity units)
|
||||
power_f (positive real)
|
||||
cutoff (distance units)
|
||||
kappa (thermal conductivity units)
|
||||
power_T (positive real)
|
||||
cutoff_T (distance units)
|
||||
optional keyword = power or kappa :ul
|
||||
|
||||
The keyword {power} or {kappa} is optional. Both "power" and "kappa"
|
||||
require 4 parameters <font size="4">c<sub>1</sub>, c<sub>2</sub>,
|
||||
c<sub>4</sub>, c<sub>4</sub></font> showing the temperature dependence
|
||||
of the exponent <center><font size="4"> <i>s</i>(<i>T</i>) =
|
||||
power_f*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
|
||||
+c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
|
||||
and of the mesoscopic heat friction <center><font size="4">
|
||||
<i>s<sub>T</sub>(T)</i> =
|
||||
kappa*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
|
||||
+c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
|
||||
If the keyword {power} or {kappa} is not specified, the eDPD system
|
||||
will use constant power_f and kappa, which is independent to
|
||||
temperature changes.
|
||||
|
||||
:line
|
||||
|
||||
The {mdpd/rhosum} style computes the local particle mass density rho
|
||||
for mDPD particles by kernel function interpolation.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the "pair_coeff"_pair_coeff.html command as in the examples above.
|
||||
|
||||
cutoff (distance units) :ul
|
||||
|
||||
:line
|
||||
|
||||
The {mdpd} style computes the many-body interactions between mDPD
|
||||
particles following the formulations in
|
||||
"(Li2013_POF)"_#Li2013_POF. The dissipative and random forces are in
|
||||
the form same as the classical DPD, but the conservative force is
|
||||
local density dependent, which are given by
|
||||
|
||||
:c,image(Eqs/pair_mdpd_force.jpg)
|
||||
|
||||
where the first term in <font size="4">F<sup>C</sup></font> with a
|
||||
negative coefficient A < 0 stands for an attractive force within an
|
||||
interaction range <font size="4">r<sub>c</sub></font>, and the second
|
||||
term with B > 0 is the density-dependent repulsive force within an
|
||||
interaction range <font size="4">r<sub>d</sub></font>.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types via the
|
||||
"pair_coeff"_pair_coeff.html command as in the examples above.
|
||||
|
||||
A (force units)
|
||||
B (force units)
|
||||
gamma (force/velocity units)
|
||||
cutoff_c (distance units)
|
||||
cutoff_d (distance units) :ul
|
||||
|
||||
:line
|
||||
|
||||
The {tdpd} style computes the pairwise interactions and chemical
|
||||
concentration fluxes for tDPD particles following the formulations in
|
||||
"(Li2015_JCP)"_#Li2015_JCP. The time evolution of a tDPD particle is
|
||||
governed by the conservation of momentum and concentration given by
|
||||
|
||||
:c,image(Eqs/pair_tdpd_gov.jpg)
|
||||
|
||||
where the three components of <font size="4">F<sub>i</sub></font>
|
||||
including the conservative force <font
|
||||
size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
|
||||
size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
|
||||
size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
|
||||
|
||||
:c,image(Eqs/pair_tdpd_force.jpg)
|
||||
|
||||
The concentration flux between two tDPD particles includes the Fickian
|
||||
flux <font size="4">Q<sub>ij</sub><sup>D</sup></font> and random flux
|
||||
<font size="4">Q<sub>ij</sub><sup>R</sup></font>, which are given by
|
||||
|
||||
:c,image(Eqs/pair_tdpd_flux.jpg)
|
||||
|
||||
where the parameters kappa and epsilon determine the strength of the
|
||||
Fickian and random fluxes. <font size="4"><i>m</i><sub>s</sub></font>
|
||||
is the mass of a single solute molecule. In general, <font
|
||||
size="4"><i>m</i><sub>s</sub></font> is much smaller than the mass of
|
||||
a tDPD particle <font size="4"><i>m</i></font>. For more details, see
|
||||
"(Li2015_JCP)"_#Li2015_JCP.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types via the
|
||||
"pair_coeff"_pair_coeff.html command as in the examples above.
|
||||
|
||||
A (force units)
|
||||
gamma (force/velocity units)
|
||||
power_f (positive real)
|
||||
cutoff (distance units)
|
||||
cutoff_CC (distance units)
|
||||
kappa_i (diffusivity units)
|
||||
epsilon_i (diffusivity units)
|
||||
power_cc_i (positive real) :ul
|
||||
|
||||
The last 3 values must be repeated Nspecies times, so that values for
|
||||
each of the Nspecies chemical species are specified, as indicated by
|
||||
the "I" suffix. In the first pair_coeff example above for pair_style
|
||||
tdpd, Nspecies = 1. In the second example, Nspecies = 2, so 3
|
||||
additional coeffs are specified (for species 2).
|
||||
|
||||
:line
|
||||
|
||||
[Example scripts]
|
||||
|
||||
There are example scripts for using all these pair styles in
|
||||
examples/USER/meso. The example for an eDPD simulation models heat
|
||||
conduction with source terms analog of periodic Poiseuille flow
|
||||
problem. The setup follows Fig.12 in "(Li2014_JCP)"_#Li2014_JCP. The
|
||||
output of the short eDPD simulation (about 2 minutes on a single core)
|
||||
gives a temperature and density profiles as
|
||||
|
||||
:c,image(JPG/examples_edpd.jpg)
|
||||
|
||||
The example for a mDPD simulation models the oscillations of a liquid
|
||||
droplet started from a liquid film. The mDPD parameters are adopted
|
||||
from "(Li2013_POF)"_#Li2013_POF. The short mDPD run (about 2 minutes
|
||||
on a single core) generates a particle trajectory which can
|
||||
be visualized as follows.
|
||||
|
||||
:c,image(JPG/examples_mdpd_first.jpg,JPG/examples_mdpd.gif)
|
||||
:c,image(JPG/examples_mdpd_last.jpg)
|
||||
|
||||
The first image is the initial state of the simulation. If you
|
||||
click it a GIF movie should play in your browser. The second image
|
||||
is the final state of the simulation.
|
||||
|
||||
The example for a tDPD simulation computes the effective diffusion
|
||||
coefficient of a tDPD system using a method analogous to the periodic
|
||||
Poiseuille flow. The tDPD system is specified with two chemical
|
||||
species, and the setup follows Fig.1 in
|
||||
"(Li2015_JCP)"_#Li2015_JCP. The output of the short tDPD simulation
|
||||
(about one and a half minutes on a single core) gives the
|
||||
concentration profiles of the two chemical species as
|
||||
|
||||
:c,image(JPG/examples_tdpd.jpg)
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support
|
||||
mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
|
||||
|
||||
The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support
|
||||
the "pair_modify"_pair_modify.html shift, table, and tail options.
|
||||
|
||||
The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not write
|
||||
information to "binary restart files"_restart.html. Thus, you need
|
||||
to re-specify the pair_style and pair_coeff commands in an input script
|
||||
that reads a restart file.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of
|
||||
the USER-MESO package. It is only enabled if LAMMPS was built with
|
||||
that package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html,
|
||||
"fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html,
|
||||
"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html,
|
||||
"compute edpd/temp/atom"_compute_edpd_temp_atom.html,
|
||||
"compute tdpd/cc/atom"_compute_tdpd_cc_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Li2014_JCP)
|
||||
[(Li2014_JCP)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys,
|
||||
265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.
|
||||
|
||||
:link(Li2015_CC)
|
||||
[(Li2015_CC)] Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040
|
||||
(2015). DOI: 10.1039/C5CC01684C.
|
||||
|
||||
:link(Li2013_POF)
|
||||
[(Li2013_POF)] Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013).
|
||||
DOI: 10.1063/1.4812366.
|
||||
|
||||
:link(Li2015_JCP)
|
||||
[(Li2015_JCP)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys,
|
||||
143: 014101 (2015). DOI: 10.1063/1.4923254.
|
||||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
pair_style multi/lucy/rx command :h3
|
||||
pair_style multi/lucy/rx/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -200,6 +201,29 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -20,20 +20,24 @@ pair_coeff * * style2 args :pre
|
|||
|
||||
style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
|
||||
|
||||
style2 = {oxdna/stk}
|
||||
args = list of arguments for these two particular styles :ul
|
||||
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
T = temperature (oxDNA units, 0.1 = 300 K) :pre
|
||||
{oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
|
||||
|
||||
|
|
@ -44,10 +48,11 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
|
|||
excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well
|
||||
as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported "(Sulc)"_#Sulc1.
|
||||
|
||||
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
|
||||
in the above example. The individual potentials consist of products of modulation factors,
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
|
||||
|
|
@ -55,9 +60,10 @@ for a detailed description of the oxDNA force field.
|
|||
|
||||
NOTE: These pair styles have to be used together with the related oxDNA bond style
|
||||
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
|
||||
"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
|
||||
Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
|
||||
and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
|
@ -86,7 +92,11 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
|
||||
:line
|
||||
|
||||
:link(Sulc1)
|
||||
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
:link(Ouldridge-DPhil1)
|
||||
[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
:link(Ouldridge1)
|
||||
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
|
|
|||
|
|
@ -21,11 +21,15 @@ pair_coeff * * style2 args :pre
|
|||
|
||||
style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
|
||||
|
||||
style2 = {oxdna2/stk} or {oxdna2/dh}
|
||||
args = list of arguments for these two particular styles :ul
|
||||
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
{oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
{oxdna2/dh} args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
|
|
@ -35,10 +39,10 @@ args = list of arguments for these two particular styles :ul
|
|||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
|
||||
|
|
@ -50,7 +54,8 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
|
|||
excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
|
||||
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
|
||||
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported "(Sulc)"_#Sulc2.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
|
|
@ -61,9 +66,10 @@ and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi
|
|||
|
||||
NOTE: These pair styles have to be used together with the related oxDNA2 bond style
|
||||
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
|
||||
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
|
||||
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
|
||||
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
|
@ -92,6 +98,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
|
||||
:line
|
||||
|
||||
:link(Sulc2)
|
||||
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
:link(Snodin)
|
||||
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
|
||||
|
||||
|
|
|
|||
|
|
@ -10,8 +10,7 @@ pair_style snap command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style snap
|
||||
:pre
|
||||
pair_style snap :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
|
|
@ -20,17 +19,16 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Pair style {snap} computes interactions
|
||||
using the spectral neighbor analysis potential (SNAP)
|
||||
"(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
|
||||
"(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
|
||||
which uses bispectrum components
|
||||
Pair style {snap} computes interactions using the spectral
|
||||
neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142.
|
||||
Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102,
|
||||
"(Bartok2013)"_#Bartok2013 which uses bispectrum components
|
||||
to characterize the local neighborhood of each atom
|
||||
in a very general way. The mathematical definition of the
|
||||
bispectrum calculation used by SNAP is identical
|
||||
to that used by "compute sna/atom"_compute_sna_atom.html.
|
||||
In SNAP, the total energy is decomposed into a sum over
|
||||
atom energies. The energy of atom {i } is
|
||||
atom energies. The energy of atom {i} is
|
||||
expressed as a weighted sum over bispectrum components.
|
||||
|
||||
:c,image(Eqs/pair_snap.jpg)
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@
|
|||
:line
|
||||
|
||||
pair_style table/rx command :h3
|
||||
pair_style table/rx/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -223,6 +224,29 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
|
|
|
|||
|
|
@ -58,6 +58,7 @@ Pair Styles :h1
|
|||
pair_meam
|
||||
pair_meam_spline
|
||||
pair_meam_sw_spline
|
||||
pair_meso
|
||||
pair_mgpt
|
||||
pair_mie
|
||||
pair_momb
|
||||
|
|
|
|||
|
|
@ -374,10 +374,9 @@ needed if new bonds (angles, dihedrals, impropers) will be added to
|
|||
the system when a simulation runs, e.g. by using the "fix
|
||||
bond/create"_fix_bond_create.html command. Using this header flag
|
||||
is deprecated; please use the {extra/bond/per/atom} keyword (and
|
||||
correspondingly for angles, dihedrals and impropers) in the
|
||||
read_data command instead. Either will pre-allocate space in LAMMPS
|
||||
data structures for storing the new bonds (angles,
|
||||
dihedrals, impropers).
|
||||
correspondingly for angles, dihedrals and impropers) in the read_data
|
||||
command instead. Either will pre-allocate space in LAMMPS data
|
||||
structures for storing the new bonds (angles, dihedrals, impropers).
|
||||
|
||||
The "extra special per atom" setting is typically only needed if new
|
||||
bonds/angles/etc will be added to the system, e.g. by using the "fix
|
||||
|
|
@ -547,6 +546,9 @@ bond: atom-ID molecule-ID atom-type x y z
|
|||
charge: atom-ID atom-type q x y z
|
||||
dipole: atom-ID atom-type q x y z mux muy muz
|
||||
dpd: atom-ID atom-type theta x y z
|
||||
edpd: atom-ID atom-type edpd_temp edpd_cv x y z
|
||||
mdpd: atom-ID atom-type x y z
|
||||
tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies
|
||||
electron: atom-ID atom-type q spin eradius x y z
|
||||
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
|
||||
full: atom-ID molecule-ID atom-type q x y z
|
||||
|
|
@ -566,12 +568,15 @@ The per-atom values have these meanings and units, listed alphabetically:
|
|||
atom-ID = integer ID of atom
|
||||
atom-type = type of atom (1-Ntype)
|
||||
bodyflag = 1 for body particles, 0 for point particles
|
||||
cc = chemical concentration for tDPD particles for each species (mole/volume units)
|
||||
contact-radius = ??? (distance units)
|
||||
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
|
||||
cv = heat capacity (need units) for SPH particles
|
||||
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
|
||||
diameter = diameter of spherical atom (distance units)
|
||||
e = energy (need units) for SPH particles
|
||||
edpd_temp = temperature for eDPD particles (temperature units)
|
||||
edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units)
|
||||
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
||||
eradius = electron radius (or fixed-core radius)
|
||||
etag = integer ID of electron that each wavepacket belongs to
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
|||
{bond} or {angle} or {dihedral} or {improper} or \
|
||||
{meso/e} or {meso/cv} or {meso/rho} or \
|
||||
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
|
||||
{i_name} or {d_name} :l
|
||||
{edpd/temp} or {edpd/cv} or {cc} or {i_name} or {d_name} :l
|
||||
{type} value = atom type
|
||||
value can be an atom-style variable (see below)
|
||||
{type/fraction} values = type fraction seed
|
||||
|
|
@ -98,6 +98,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
|||
{dpd/theta} value = internal temperature of DPD particles (temperature units)
|
||||
value can be an atom-style variable (see below)
|
||||
value can be NULL which sets internal temp of each particle to KE temp
|
||||
{edpd/temp} value = temperature of eDPD particles (temperature units)
|
||||
value can be an atom-style variable (see below)
|
||||
{edpd/cv} value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
|
||||
value can be an atom-style variable (see below)
|
||||
{cc} values = index cc
|
||||
index = index of a chemical species (1 to Nspecies)
|
||||
cc = chemical concentration of tDPD particles for a species (mole/volume units)
|
||||
{i_name} value = value for custom integer vector with name
|
||||
{d_name} value = value for custom floating-point vector with name :pre
|
||||
:ule
|
||||
|
|
@ -418,6 +425,19 @@ value >= 0.0, the internal temperature is set to that value. If it is
|
|||
< 0.0, the computation of Tkin is performed and the internal
|
||||
temperature is set to that value.
|
||||
|
||||
Keywords {edpd/temp} and {edpd/cv} set the temperature and volumetric
|
||||
heat capacity of an eDPD particle as defined by the USER-MESO package.
|
||||
Currently, only "atom_style edpd"_atom_style.html defines particles
|
||||
with these attributes. The values for the temperature and heat
|
||||
capacity must be positive.
|
||||
|
||||
Keyword {cc} sets the chemical concentration of a tDPD particle for a
|
||||
specified species as defined by the USER-MESO package. Currently, only
|
||||
"atom_style tdpd"_atom_style.html defines particles with this
|
||||
attribute. An integer for "index" selects a chemical species (1 to
|
||||
Nspecies) where Nspecies is set by the atom_style command. The value
|
||||
for the chemical concentration must be >= 0.0.
|
||||
|
||||
Keywords {i_name} and {d_name} refer to custom integer and
|
||||
floating-point properties that have been added to each atom via the
|
||||
"fix property/atom"_fix_property_atom.html command. When that command
|
||||
|
|
|
|||
|
|
@ -25,9 +25,7 @@ keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {c
|
|||
{coul} values = w1,w2,w3
|
||||
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
|
||||
{angle} value = {yes} or {no}
|
||||
{dihedral} value = {yes} or {no}
|
||||
{extra} value = N
|
||||
N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
|
||||
{dihedral} value = {yes} or {no} :pre
|
||||
:ule
|
||||
|
||||
Examples:
|
||||
|
|
@ -36,8 +34,7 @@ special_bonds amber
|
|||
special_bonds charmm
|
||||
special_bonds fene dihedral no
|
||||
special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
|
||||
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
|
||||
special_bonds lj/coul 0 1 1 extra 2 :pre
|
||||
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -178,14 +175,6 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
|
|||
of 1.0). If the {dihedral} keyword is specified as {no} which is the
|
||||
default, then the 2,5 interaction will also be weighted by 0.5.
|
||||
|
||||
The {extra} keyword can be used when additional bonds will be created
|
||||
during a simulation run, e.g. by the "fix
|
||||
bond/create"_fix_bond_create.html command. It can also be used if
|
||||
molecules will be added to the system, e.g. via the "fix
|
||||
deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
|
||||
will have atoms with more special neighbors than any atom in the
|
||||
current system has.
|
||||
|
||||
:line
|
||||
|
||||
NOTE: LAMMPS stores and maintains a data structure with a list of the
|
||||
|
|
@ -194,8 +183,9 @@ the system). If new bonds are created (or molecules added containing
|
|||
atoms with more special neighbors), the size of this list needs to
|
||||
grow. Note that adding a single bond always adds a new 1st neighbor
|
||||
but may also induce *many* new 2nd and 3rd neighbors, depending on the
|
||||
molecular topology of your system. Using the {extra} keyword leaves
|
||||
empty space in the list for this N additional 1st, 2nd, or 3rd
|
||||
molecular topology of your system. Using the {extra/special/per/atom}
|
||||
keyword to either "read_data"_read_data.html or "create_box"_create_box.html
|
||||
reserves empty space in the list for this N additional 1st, 2nd, or 3rd
|
||||
neighbors to be added. If you do not do this, you may get an error
|
||||
when bonds (or molecules) are added.
|
||||
|
||||
|
|
@ -203,8 +193,7 @@ when bonds (or molecules) are added.
|
|||
|
||||
NOTE: If you reuse this command in an input script, you should set all
|
||||
the options you need each time. This command cannot be used a 2nd
|
||||
time incrementally, e.g. to add some extra storage locations via the
|
||||
{extra} keyword. E.g. these two commands:
|
||||
time incrementally. E.g. these two commands:
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0
|
||||
special_bonds coul 0.0 0.0 1.0
|
||||
|
|
@ -221,25 +210,6 @@ Coul: coul 0.0 0.0 1.0
|
|||
because the LJ settings are reset to their default values
|
||||
each time the command is issued.
|
||||
|
||||
Likewise
|
||||
|
||||
special_bonds amber
|
||||
special_bonds extra 2 :pre
|
||||
|
||||
is not the same as this single command:
|
||||
|
||||
special_bonds amber extra 2 :pre
|
||||
|
||||
since in the former case, the 2nd command will reset all the LJ and
|
||||
Coulombic weights to 0.0 (the default).
|
||||
|
||||
One exception to this rule is the {extra} option itself. It is not
|
||||
reset to its default value of 0 each time the special_bonds command is
|
||||
invoked. This is because it can also be set by the
|
||||
"read_data"_read_data.html and "create_box"_create_box.html commands,
|
||||
so this command will not override those settings unless you explicitly
|
||||
use {extra} as an option.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -0,0 +1,67 @@
|
|||
"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
|
||||
temper/npt command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
temper/npt N M temp fix-ID seed1 seed2 pressure index :pre
|
||||
|
||||
N = total # of timesteps to run
|
||||
M = attempt a tempering swap every this many steps
|
||||
temp = initial temperature for this ensemble
|
||||
fix-ID = ID of the fix that will control temperature and pressure during the run
|
||||
seed1 = random # seed used to decide on adjacent temperature to partner with
|
||||
seed2 = random # seed for Boltzmann factor in Metropolis swap
|
||||
pressure = setpoint pressure for the ensemble
|
||||
index = which temperature (0 to N-1) I am simulating (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
temper/npt 100000 100 $t nptfix 0 58728 1
|
||||
temper/npt 2500000 1000 300 nptfix 0 32285 $p
|
||||
temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Run a parallel tempering or replica exchange simulation using multiple
|
||||
replicas (ensembles) of a system in the isothermal-isobaric (NPT)
|
||||
ensemble. The command temper/npt works like "temper"_temper.html but
|
||||
requires running replicas in the NPT ensemble instead of the canonical
|
||||
(NVT) ensemble and allows for pressure to be set in the ensembles.
|
||||
These multiple ensembles can run in parallel at different temperatures
|
||||
or different pressures. The acceptance criteria for temper/npt is
|
||||
specific to the NPT ensemble and can be found in references
|
||||
"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2.
|
||||
|
||||
Apart from the difference in acceptance criteria and the specification
|
||||
of pressure, this command works much like the "temper"_temper.html
|
||||
command. See the documentation on "temper"_temper.html for information
|
||||
on how the parallel tempering is handled in general.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command can only be used if LAMMPS was built with the USER-MISC
|
||||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info on packages.
|
||||
|
||||
This command should be used with a fix that maintains the
|
||||
isothermal-isobaric (NPT) ensemble.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"temper"_temper.html, "variable"_variable.html, "fix_npt"_fix_nh.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(Okabe2)
|
||||
[(Okabe)] T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
|
||||
|
||||
:link(Mori2)
|
||||
[(Mori)] Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).
|
||||
|
|
@ -176,12 +176,13 @@ By recognizing the fix {drude}, LAMMPS will find and store matching
|
|||
DC-DP pairs and will treat DP as equivalent to their DC in the
|
||||
{special bonds} relations. It may be necessary to extend the space
|
||||
for storing such special relations. In this case extra space should
|
||||
be reserved by using the {extra} keyword of the {special_bonds}
|
||||
be reserved by using the {extra/special/per/atom} keyword of either
|
||||
the "read_data"_read_data.html or "create_box"_create_box.html
|
||||
command. With our phenol, there is 1 more special neighbor for which
|
||||
space is required. Otherwise LAMMPS crashes and gives the required
|
||||
value.
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5 extra 1 :pre
|
||||
read_data data-p.lmp extra/special/per/atom 1 :pre
|
||||
|
||||
Let us assume we want to run a simple NVT simulation at 300 K. Note
|
||||
that Drude oscillators need to be thermalized at a low temperature in
|
||||
|
|
|
|||
|
|
@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
|
|
|
|||
|
|
@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
|
|
|||
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Reference in New Issue