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This commit is contained in:
jtclemm
2024-06-24 14:09:33 -06:00
parent 2aacc017cb cfcd2b2068
commit b219bb8de8
2229 changed files with 152287 additions and 82970 deletions
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10
.github/CODEOWNERS vendored
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@ -37,7 +37,8 @@ src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde @rohskopf
src/ML-POD/* @exapde
src/ML-UF3/* @monk-04
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -65,10 +66,15 @@ src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
# core LAMMPS classes
src/lammps.* @sjplimp
@ -80,7 +86,7 @@ src/bond.* @sjplimp
src/comm*.* @sjplimp
src/compute.* @sjplimp
src/dihedral.* @sjplimp
src/domain.* @sjplimp
src/domain.* @sjplimp @stanmoore1
src/dump*.* @sjplimp
src/error.* @sjplimp
src/finish.* @sjplimp

2
.github/workflows/coverity.yml vendored
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@ -25,7 +25,7 @@ jobs:
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

6
.github/workflows/unittest-macos.yml vendored
View File

@ -15,7 +15,7 @@ jobs:
build:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
runs-on: macos-13
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
@ -32,7 +32,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}
@ -43,6 +43,8 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m venv macosenv
source macosenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \

78
cmake/CMakeLists.txt
View File

@ -120,6 +120,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
set(CMAKE_TUNE_DEFAULT "-Minform=severe")
endif()
# this hack is required to compile fmt lib with CrayClang version 15.0.2
# CrayClang is only directly recognized by version 3.28 and later
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
endif()
endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@ -209,6 +222,10 @@ endif()
add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
# re-export all symbols for plugins
if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
endif()
install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@ -239,6 +256,7 @@ set(STANDARD_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -268,6 +286,7 @@ set(STANDARD_PACKAGES
ML-RANN
ML-SNAP
ML-POD
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -416,6 +435,7 @@ if(BUILD_OMP)
(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@ -426,6 +446,21 @@ if(BUILD_OMP)
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
# this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
# CrayClang is only directly recognized by version 3.28 and later
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
endif()
endif()
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
@ -540,12 +575,12 @@ endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
foreach(HEADER cmath)
check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
endif(NOT FOUND_${HEADER})
endforeach(HEADER)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
check_include_file_cxx(cmath FOUND_CMATH)
if(NOT FOUND_CMATH)
message(FATAL_ERROR "Could not find the required 'cmath' header")
endif(NOT FOUND_CMATH)
endif()
# make the standard math library overrideable and autodetected (for systems that don't have it)
find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
@ -657,7 +692,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -972,14 +1007,15 @@ if(PKG_KOKKOS)
endif()
endif()
if(PKG_KSPACE)
if (LMP_HEFFTE)
if (FFT_USE_HEFFTE)
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: heFFTe")
if (HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
if (FFT_HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${FFT_HEFFTE_BACKEND}")
else()
message(STATUS "heFFTe backend: stock (builtin FFT implementation, tested for corrected but not optimized for production)")
endif()
message(STATUS "Using distributed FFT algorithms from heFTTe")
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
@ -998,28 +1034,10 @@ if(PKG_KSPACE)
else()
message(STATUS "Using non-threaded FFTs")
endif()
if (FFT_HEFFTE)
message(STATUS "Using distributed algorithms from heFTTe")
else()
message(STATUS "Using builtin distributed algorithms")
message(STATUS "Using builtin distributed FFT algorithms")
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: cuFFT")
endif()
elseif(Kokkos_ENABLE_HIP)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: hipFFT")
endif()
else()
message(STATUS "Kokkos FFT: ${FFT}")
endif()
endif()
message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
endif()
endif()
if(BUILD_DOC)

10
cmake/Modules/DetectHIPInstallation.cmake
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@ -1,11 +1,3 @@
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
"Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
@ -13,4 +5,4 @@ if(NOT DEFINED ROCM_PATH)
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

2
cmake/Modules/ExternalCMakeProject.cmake
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@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
"${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
endif()
add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
"${CMAKE_BINARY_DIR}/_deps/${target}-build")
"${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
endfunction(ExternalCMakeProject)

5
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)
@ -8,4 +8,3 @@ set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
include(ExternalCMakeProject)
ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
add_library(OpenCL::OpenCL ALIAS OpenCL)

9
cmake/Modules/Packages/DPD-BASIC.cmake Normal file
View File

@ -0,0 +1,9 @@
# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

7
cmake/Modules/Packages/GPU.cmake
View File

@ -1,3 +1,10 @@
# Silence CMake warnings about FindCUDA being obsolete.
# We may need to eventually rewrite this section to use enable_language(CUDA)
if(POLICY CMP0146)
cmake_policy(SET CMP0146 OLD)
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

3
cmake/Modules/Packages/INTEL.cmake
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@ -111,6 +111,9 @@ if(PKG_KSPACE)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
if(PKG_ML-SNAP)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/sna_intel.cpp)
endif()
target_sources(lammps PRIVATE ${INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

33
cmake/Modules/Packages/KOKKOS.cmake
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@ -45,8 +45,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.2.00 REQUIRED CONFIG)
find_package(Kokkos 4.3.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -126,16 +126,33 @@ if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(NOT (FFT STREQUAL "KISS"))
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
if(NOT (FFT STREQUAL "KISS"))
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "HIPFFT")
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
endif()

37
cmake/Modules/Packages/KSPACE.cmake
View File

@ -48,10 +48,15 @@ endif()
option(FFT_USE_HEFFTE "Use heFFTe as the distributed FFT engine, overrides the FFT option." OFF)
if(FFT_USE_HEFFTE)
# if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
# if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
# map standard FFT choices to available heFFTe backends: FFTW3 -> FFTW, KISS -> BUILTIN
set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL BUILTIN)
string(REPLACE FFTW3 FFTW FFT_HEFFTE_BACKEND_DEFAULT ${FFT})
string(REPLACE KISS BUILTIN FFT_HEFFTE_BACKEND_DEFAULT ${FFT_HEFFTE_BACKEND_DEFAULT})
set(FFT_HEFFTE_BACKEND "${FFT_HEFFTE_BACKEND_DEFAULT}" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
validate_option(FFT_HEFFTE_BACKEND FFT_HEFFTE_BACKEND_VALUES)
if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
set(HEFFTE_COMPONENTS "FFTW")
@ -60,24 +65,38 @@ if(FFT_USE_HEFFTE)
set(HEFFTE_COMPONENTS "MKL")
set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
else()
set(HEFFTE_COMPONENTS "BUILTIN")
message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
endif()
find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
if (NOT Heffte_FOUND) # download and build
if(BUILD_SHARED_LIBS)
set(BUILD_SHARED_LIBS_WAS_ON YES)
set(BUILD_SHARED_LIBS OFF)
endif()
if(CMAKE_REQUEST_PIC)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
set(Heffte_ENABLE_${FFT_HEFFTE_BACKEND} ON)
include(FetchContent)
FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
URL "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
)
FetchContent_Populate(HEFFTE_PROJECT)
add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
target_link_libraries(Heffte::Heffte INTERFACE Heffte)
endif()
# fixup git hash to show "(unknown)" to avoid compilation failures.
file(READ ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h HEFFTE_CFG_FILE_TEXT)
string(REPLACE "@Heffte_GIT_HASH@" "(unknown)" HEFFTE_CFG_FILE_TEXT "${HEFFTE_CFG_FILE_TEXT}")
file(WRITE ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h "${HEFFTE_CFG_FILE_TEXT}")
add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR} EXCLUDE_FROM_ALL)
add_library(Heffte::Heffte ALIAS Heffte)
if(BUILD_SHARED_LIBS_WAS_ON)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
target_link_libraries(lammps PRIVATE Heffte::Heffte)
endif()

4
cmake/Modules/Packages/MDI.cmake
View File

@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)

15
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -10,6 +10,14 @@ endif()
option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
set(MLIAP_ENABLE_ACE_DEFAULT OFF)
if(PKG_ML-PACE)
set(MLIAP_ENABLE_ACE_DEFAULT ON)
endif()
option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
find_package(Python COMPONENTS NumPy REQUIRED)
@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON)
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif()
if(MLIAP_ENABLE_ACE)
if(NOT PKG_ML-PACE)
message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
endif()
target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
endif()

6
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -18,7 +18,9 @@ if(DOWNLOAD_QUIP)
set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
# quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
@ -56,7 +58,7 @@ if(DOWNLOAD_QUIP)
GIT_SUBMODULES "src/fox;src/GAP"
PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

20
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,5 +1,9 @@
# Plumed2 support for PLUMED package
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -21,9 +25,11 @@ else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -151,15 +157,15 @@ else()
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")

2
cmake/packaging/build_linux_tgz.sh
View File

@ -59,12 +59,14 @@ done
echo "Set up wrapper script"
MYDIR=$(dirname "$0")
cp ${MYDIR}/xdg-open ${DESTDIR}/bin
cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
for s in ${DESTDIR}/bin/*
do \
EXE=$(basename $s)
test ${EXE} = linux_wrapper.sh && continue
test ${EXE} = qt.conf && continue
test ${EXE} = xdg-open && continue
ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
done

14
cmake/packaging/linux_wrapper.sh
View File

@ -4,15 +4,17 @@
# reset locale to avoid problems with decimal numbers
export LC_ALL=C
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")
BASEDIR="$(dirname "$0")"
EXENAME="$(basename "$0")"
PATH="${BASEDIR}/bin:${PATH}"
# append to LD_LIBRARY_PATH to prefer local (newer) libs
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
# set some environment variables for LAMMPS etc.
LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
exec "${BASEDIR}/bin/${EXENAME}" "$@"

1074
cmake/packaging/xdg-open Executable file
View File

File diff suppressed because it is too large Load Diff

2
cmake/presets/all_off.cmake
View File

@ -28,6 +28,7 @@ set(ALL_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -60,6 +61,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

2
cmake/presets/all_on.cmake
View File

@ -30,6 +30,7 @@ set(ALL_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -62,6 +63,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

3
cmake/presets/kokkos-cuda.cmake
View File

@ -9,5 +9,8 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "CUFFT" CACHE STRING "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

3
cmake/presets/kokkos-hip.cmake
View File

@ -12,6 +12,9 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

2
cmake/presets/mingw-cross.cmake
View File

@ -24,6 +24,7 @@ set(WIN_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -50,6 +51,7 @@ set(WIN_PACKAGES
ML-POD
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

2
cmake/presets/most.cmake
View File

@ -26,6 +26,7 @@ set(ALL_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -45,6 +46,7 @@ set(ALL_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
OPENMP

2
cmake/presets/windows.cmake
View File

@ -22,6 +22,7 @@ set(WIN_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -42,6 +43,7 @@ set(WIN_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

3
doc/Makefile
View File

@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -231,6 +233,7 @@ role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\

6
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "21 November 2023" "2023-11-21"
.TH LAMMPS "1" "17 April 2024" "2024-04-17"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 21 November 2023
\- Molecular Dynamics Simulator. Version 17 April 2024
.SH SYNOPSIS
.B lmp
@ -297,7 +297,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2022 Sandia Corporation
© 2003--2024 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

3
doc/src/Bibliography.rst
View File

@ -877,6 +877,9 @@ Bibliography
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Pavlov)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

78
doc/src/Build_development.rst
View File

@ -122,32 +122,39 @@ Code Coverage and Unit Testing (CMake only)
-------------------------------------------
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
on various platforms and with a variety of settings), unit testing
(i.e. whether certain individual parts of the code produce the expected
results for given inputs), run testing (whether selected complete input
decks run without crashing for multiple configurations), and regression
testing (i.e. whether selected input examples reproduce the same
results over a given number of steps and operations within a given
error margin). The status of this automated testing can be viewed on
`https://ci.lammps.org <https://ci.lammps.org>`_.
during development:
- Integration testing (i.e. whether the code compiles
on various platforms and with a variety of compilers and settings),
- Unit testing (i.e. whether certain functions or classes of the code
produce the expected results for given inputs),
- Run testing (i.e. whether selected input decks can run to completion
without crashing for multiple configurations),
- Regression testing (i.e. whether selected input examples reproduce the
same results over a given number of steps and operations within a
given error margin).
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub.
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
It requires the `YAML <https://pyyaml.org/>`_ library and matching
development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
.. admonition:: Software version requirements for testing
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
The compiler and library version requirements for the testing
@ -155,7 +162,7 @@ for implementing the tests.
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect incompatible versions and either skip incompatible tests or
stop with an error. Also the number of tests will depend on
stop with an error. Also the number of available tests will depend on
installed LAMMPS packages, development environment, operating system,
and configuration settings.
@ -234,12 +241,31 @@ will be skipped if prerequisite features are not available in LAMMPS.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests for styles of the same kind of style (e.g. pair styles or bond
styles) are performed with the same test executable using different
input files in YAML format. So to add a test for another style of the
same kind it may be sufficient to add a suitable YAML file.
:doc:`Detailed instructions for adding tests <Developer_unittest>` are
provided in the Programmer Guide part of the manual.
Tests as shown by the ``ctest`` program are command lines defined in the
``CMakeLists.txt`` files in the ``unittest`` directory tree. A few
tests simply execute LAMMPS with specific command line flags and check
the output to the screen for expected content. A large number of unit
tests are special tests programs using the `GoogleTest framework
<https://github.com/google/googletest/>`_ and linked to the LAMMPS
library that test individual functions or create a LAMMPS class
instance, execute one or more commands and check data inside the LAMMPS
class hierarchy. There are also tests for the C-library, Fortran, and
Python module interfaces to LAMMPS. The Python tests use the Python
"unittest" module in a similar fashion than the others use `GoogleTest`.
These special test programs are structured to perform multiple
individual tests internally and each of those contains several checks
(aka assertions) for internal data being changed as expected.
Tests for force computing or modifying styles (e.g. styles for non-bonded
and bonded interactions and selected fixes) are run by using a more generic
test program that reads its input from files in YAML format. The YAML file
provides the information on how to customized the test program to test
a specific style and - if needed - with specific settings.
To add a test for another, similar style (e.g. a new pair style) it is
usually sufficient to add a suitable YAML file. :doc:`Detailed
instructions for adding tests <Developer_unittest>` are provided in the
Programmer Guide part of the manual. A description of what happens
during the tests is given below.
Unit tests for force styles
^^^^^^^^^^^^^^^^^^^^^^^^^^^

14
doc/src/Build_extras.rst
View File

@ -533,9 +533,6 @@ They must be specified in uppercase.
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
@ -566,18 +563,15 @@ They must be specified in uppercase.
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - BGQ
- HOST
- IBM Blue Gene/Q CPU
* - POWER7
- HOST
- IBM POWER7 CPU
* - POWER8
- HOST
- IBM POWER8 CPU
* - POWER9
- HOST
- IBM POWER9 CPU
* - RISCV_SG2042
- HOST
- SG2042 (RISC-V) CPU
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
@ -666,7 +660,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.2 of the Kokkos library.
This list was last updated for version 4.3.0 of the Kokkos library.
.. tabs::

29
doc/src/Build_settings.rst
View File

@ -44,7 +44,7 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS, but other libraries can be faster.
LAMMPS can use them if they are available on your system.
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Alternatively, LAMMPS can use the `heFFTe
<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
@ -59,15 +59,19 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
.. note::
The values for the FFT variable must be in upper-case. This is
an exception to the rule that all CMake variables can be specified
with lower-case values.
When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos,
you must use either CUFFT or KISS.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
@ -106,6 +110,8 @@ libraries and better pipelining for packing and communication.
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
@ -116,6 +122,8 @@ libraries and better pipelining for packing and communication.
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
@ -178,6 +186,11 @@ The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
above).
The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
AMD's HIP installations, respectively. These FFT libraries require the
Kokkos acceleration package to be enabled and the Kokkos back end to be
GPU-resident (i.e., HIP or CUDA).
Performing 3d FFTs in parallel can be time-consuming due to data access
and required communication. This cost can be reduced by performing
single-precision FFTs instead of double precision. Single precision
@ -189,11 +202,11 @@ generally less than the difference in precision. Using the
``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
use and parallel communication costs for transposing 3d FFT data.
When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
library a second time with support for single-precision.
When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
the FFTW3 installation includes support for single-precision.
For FFTW3, do the following, which should produce the additional
library ``libfftw3f.a`` or ``libfftw3f.so``\ .
When compiler FFTW3 from source, you can do the following, which should
produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
.. code-block:: bash

6
doc/src/Commands_bond.rst
View File

@ -27,7 +27,7 @@ OPT.
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
* :doc:`hybrid (k) <bond_hybrid>`
*
*
*
@ -90,6 +90,7 @@ OPT.
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
@ -125,9 +126,10 @@ OPT.
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`

2
doc/src/Commands_fix.rst
View File

@ -61,6 +61,7 @@ OPT.
* :doc:`controller <fix_controller>`
* :doc:`damping/cundall <fix_damping_cundall>`
* :doc:`deform (k) <fix_deform>`
* :doc:`deform/pressure <fix_deform_pressure>`
* :doc:`deposit <fix_deposit>`
* :doc:`dpd/energy (k) <fix_dpd_energy>`
* :doc:`drag <fix_drag>`
@ -267,6 +268,7 @@ OPT.
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
* :doc:`wall/colloid <fix_wall>`
* :doc:`wall/ees <fix_wall_ees>`
* :doc:`wall/flow (k) <fix_wall_flow>`
* :doc:`wall/gran (k) <fix_wall_gran>`
* :doc:`wall/gran/region <fix_wall_gran_region>`
* :doc:`wall/harmonic <fix_wall>`

18
doc/src/Commands_pair.rst
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@ -25,16 +25,16 @@ OPT.
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>`
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -94,9 +94,10 @@ OPT.
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -146,7 +147,7 @@ OPT.
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
@ -245,6 +246,7 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
@ -256,6 +258,7 @@ OPT.
* :doc:`rann <pair_rann>`
* :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`rheo <pair_rheo>`
* :doc:`rheo/solid <pair_rheo_solid>`
@ -269,7 +272,7 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`soft (gko) <pair_soft>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj (g) <pair_sph_lj>`
@ -303,6 +306,7 @@ OPT.
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`uf3 (k) <pair_uf3>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`

10
doc/src/Commands_removed.rst
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@ -129,7 +129,7 @@ USER-REAXC.
USER-REAXC package
------------------
.. deprecated:: TBD
.. deprecated:: 7Feb2024
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
@ -148,6 +148,14 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
i-PI tool
---------
.. versionchanged:: TBD
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPi via pip are provided.
restart2data tool
-----------------

47
doc/src/Developer_updating.rst
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@ -18,6 +18,7 @@ Available topics in mostly chronological order are:
- `Setting flags in the constructor`_
- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::count_words() functions instead of atom->count_words()`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
@ -130,6 +131,41 @@ Not applying this change will not cause a compilation error, but
can lead to inconsistent behavior and incorrect tallying of
energy or virial.
Use utils::count_words() functions instead of atom->count_words()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 2Jun2020
The "count_words()" functions for parsing text have been moved from the
Atom class to the :doc:`utils namespace <Developer_utils>`. The
"count_words()" function in "utils" uses the Tokenizer class internally
to split a line into words and count them, thus it will not modify the
argument string as the function in the Atoms class did and thus had a
variant using a copy buffer. Unlike the old version, the new version
does not remove comments. For that you can use the
:cpp:func:`utils::trim_comment() function
<LAMMPS_NS::utils::trim_comment>` as shown in the example below.
Old:
.. code-block:: c++
nwords = atom->count_words(line);
int nwords = atom->count_words(buf);
New:
.. code-block:: c++
nwords = utils::count_words(line);
int nwords = utils::count_words(utils::trim_comment(buf));
.. seealso::
:cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
:cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
Use utils::numeric() functions instead of force->numeric()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -137,11 +173,12 @@ Use utils::numeric() functions instead of force->numeric()
The "numeric()" conversion functions (including "inumeric()",
"bnumeric()", and "tnumeric()") have been moved from the Force class to
the utils namespace. Also they take an additional argument that selects
whether the ``Error::all()`` or ``Error::one()`` function should be
called in case of an error. The former should be used when *all* MPI
processes call the conversion function and the latter *must* be used
when they are called from only one or a subset of the MPI processes.
the :doc:`utils namespace <Developer_utils>`. Also they take an
additional argument that selects whether the ``Error::all()`` or
``Error::one()`` function should be called in case of an error. The
former should be used when *all* MPI processes call the conversion
function and the latter *must* be used when they are called from only
one or a subset of the MPI processes.
Old:

4
doc/src/Developer_utils.rst
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@ -635,10 +635,10 @@ Tohoku University (under MIT license)
----------
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
:project: progguide
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
:project: progguide
---------------------------

49
doc/src/Errors_details.rst
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@ -13,15 +13,44 @@ discussions of such cases.
Unknown identifier in data file
-------------------------------
This error happens when LAMMPS encounters a line of text in an unexpected format
while reading a data file. This is most commonly cause by inconsistent header and
section data. The header section informs LAMMPS how many entries or lines are expected in the
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
or stop reading before the section has ended.
This error happens when LAMMPS encounters a line of text with an
unexpected keyword while :doc:`reading a data file <read_data>`. This
would be either header keywords or section header keywords. This is
most commonly due to a mistyped keyword or due to a keyword that is
inconsistent with the :doc:`atom style <atom_style>` used.
Such a mismatch can happen unexpectedly when the first line of the data
is *not* a comment as required by the format. That would result in
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
is treated as a comment.
The header section informs LAMMPS how many entries or lines are expected
in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
the data file. If there is a mismatch, LAMMPS will either keep reading
beyond the end of a section or stop reading before the section has
ended. In that case the next line will not contain a recognized keyword.
Such a mismatch can also happen when the first line of the data
is *not* a comment as required by the format, but a line with a valid
header keyword. That would result in LAMMPS expecting, for instance,
0 atoms because the "atoms" header line is the first line and thus
treated as a comment.
Another possibility to trigger this error is to have a keyword in the
data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
but the :doc:`read_data <read_data>` command is missing the (optional)
arguments that identify the fix and the header keyword and section
keyword or those arguments are inconsistent with the keywords in the
data file.
.. _err0002:
Incorrect format in ... section of data file
--------------------------------------------
This error happens when LAMMPS reads the contents of a section of a
:doc:`data file <read_data>` and the number of parameters in the line
differs from what is expected. This most commonly happens, when the
atom style is different from what is expected for a specific data file
since changing the atom style usually changes the format of the line.
This error can also happen when the number of entries indicated in the
header of a data file (e.g. the number of atoms) is larger than the
number of lines provided (e.g. in the corresponding Atoms section)
and then LAMMPS will continue reading into the next section and that
would have a completely different format.

6
doc/src/Errors_messages.rst
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@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
*Triclinic box skew is too large*
The displacement in a skewed direction must be less than half the box
length in that dimension. E.g. the xy tilt must be between -half and
+half of the x box length. This constraint can be relaxed by using
the box tilt command.
*Tried to convert a double to int, but input_double > INT_MAX*
Self-explanatory.

7
doc/src/Errors_warnings.rst
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@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations.
More than the maximum # of neighbors was found multiple times. This
was unexpected.
*Triclinic box skew is large*
The displacement in a skewed direction is normally required to be less
than half the box length in that dimension. E.g. the xy tilt must be
between -half and +half of the x box length. You have relaxed the
constraint using the box tilt command, but the warning means that a
LAMMPS simulation may be inefficient as a result.
*Use special bonds = 0,1,1 with bond style fene*
Most FENE models need this setting for the special_bonds command.

51
doc/src/Fortran.rst
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@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_setting: function
:f extract_global: :f:func:`extract_global`
:ftype extract_global: function
:f map_atom: :f:func:`map_atom`
:ftype map_atom: function
:f extract_atom: :f:func:`extract_atom`
:ftype extract_atom: function
:f extract_compute: :f:func:`extract_compute`
@ -315,6 +317,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_variable: function
:f set_variable: :f:subr:`set_variable`
:ftype set_variable: subroutine
:f set_string_variable: :f:subr:`set_set_string_variable`
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -1251,8 +1257,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
three elements of the global vector calculated by fix recenter into the
variables *dx*, *dy*, and *dz*, respectively.
If asked for per-atom or local data, :f:func:`extract_compute` returns a
pointer to actual LAMMPS data. The pointer so returned will have the
If asked for per-atom or local data, :f:func:`extract_fix` returns a
pointer to actual LAMMPS data. The pointer returned will have the
appropriate size to match the internal data, and will be
type/kind/rank-checked at the time of the assignment. For example,
@ -1398,7 +1404,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Set the value of a string-style variable.
.. versionadded:: 3Nov2022
.. deprecated:: 7Feb2024
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
variable, an error is generated.
.. warning::
This subroutine is deprecated and :f:subr:`set_string_variable`
should be used instead.
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
--------
.. f:subroutine:: set_string_variable(name, str)
Set the value of a string-style variable.
.. versionadded:: 7Feb2024
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
@ -1406,7 +1433,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
:to: :cpp:func:`lammps_set_string_variable`
--------
.. f:subroutine:: set_internal_variable(name, val)
Set the value of a internal-style variable.
.. versionadded:: 7Feb2024
This function assigns a new value from the floating-point number *val* to
the internal-style variable *name*\ . If *name* does not exist or is not
an internal-style variable, an error is generated.
:p character(len=*) name: name of the variable
:p read(c_double) val: new value to assign to the variable
:to: :cpp:func:`lammps_set_internal_variable`
--------

122
doc/src/Howto_2d.rst
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@ -1,42 +1,112 @@
================
2d simulations
==============
================
Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
You must use the :doc:`dimension <dimension>` command to specify a 2d
simulation. The default is 3d.
Make the simulation box periodic in z via the :doc:`boundary <boundary>`
command. This is the default.
A 2d simulation box must be periodic in z as set by the :doc:`boundary
<boundary>` command. This is the default.
If using the :doc:`create_box <create_box>` command to define a
simulation box, set the z dimensions narrow, but finite, so that the
:doc:`create_atoms <create_atoms>` command will fill the 3d simulation
box with a single z plane of atoms - e.g.
Simulation boxes in LAMMPS can be either orthogonal or triclinic in
shape. Orthogonal boxes in 2d are a rectangle with 4 edges that are
each perpendicular to either the x or y coordinate axes. Triclinic
boxes in 2d are a parallelogram with opposite pairs of faces parallel
to each other. LAMMPS supports two forms of triclinic boxes,
restricted and general, which for 2d differ in how the box is oriented
with respect to the xy coordinate axes. See the :doc:`Howto triclinic
<Howto_triclinic>` for a detailed description of all 3 kinds of
simulation boxes.
Here are examples of using the :doc:`create_box <create_box>` command
to define the simulation box for a 2d system.
.. code-block:: LAMMPS
create_box 1 -10 10 -10 10 -0.25 0.25
# 2d orthogonal box using a block-style region
region mybox block -10 10 0 10 -0.5 0.5
create_box 1 mybox
If using the :doc:`read_data <read_data>` command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
# 2d restricted triclinic box using a prism-style region with only xy tilt
region mybox prism 0 10 0 10 -0.5 0.5 2.0 0.0 0.0
create_box 1 mybox
Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
defined fix to ensure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
# 2d general triclinic box using a primitive cell for a 2d hex lattice
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
create_box 1 NULL 0 5 0 5 -0.5 0.5
Many of the example input scripts included in the LAMMPS distribution
Note that for 2d orthogonal or restricted triclinic boxes, the box has
a 3rd dimension which must straddle z = 0.0 in the z dimension.
Typically the width of box in the z dimension should be narrow,
e.g. -0.5 to 0.5, but that is not required. For a 2d general
triclinic box, the *a3* vector defined by the :doc:`lattice <lattice>`
command must be (0.0,0.0,1.0), which is its default value. Also the
*clo* and *chi* arguments of the :doc:`create_box <create_box>`
command must be -0.5 and 0.5.
Here are examples of using the :doc:`read_data <read_data>` command
to define the simulation box for a 2d system via keywords in the
header section of the data file. These are the same boxes as the examples
for the :doc:`create_box <create_box>` command
.. code-block:: LAMMPS
# 2d orthogonal box
-10 10 xlo xhi
0 10 ylo yhi
-0.5 0.5 zlo zhi # this is the default, so no need to specify
# 2d restricted triclinic box with only xy tilt
-10 10 xlo xhi
0 10 ylo yhi
-0.5 0.5 zlo zhi # this is the default, so no need to specify
2.0 0.0 0.0 xy xz yz
# 3d general triclinic box using a primitive cell for a 2d hex lattice
5 0 0 avec
2.5 4.3301270189 0 bvec
0 0 1 cvec # this is the default, so no need to specify
0 0 -0.5 abc origin # this is the default for 2d, so no need to specify
Note that for 2d orthogonal or restricted triclinic boxes, the box has
a 3rd dimension specified by the *zlo zhi* values, which must straddle
z = 0.0. Typically the width of box in the z dimension should be
narrow, e.g. -0.5 to 0.5, but that is not required. For a 2d general
triclinic box, the z component of *avec* and *bvec* must be zero, and
*cvec* must be (0,0,1), which is the default. The z component of *abc
origin* must also be -0.5, which is the default.
If using the :doc:`create_atoms <create_atoms>` command to create
atoms in the 2d simulation box, all the z coordinates of created atoms
will be zero.
If using the :doc:`read_data <read_data>` command to read in a data
file of atom coordinates for a 2d system, the z coordinates of all
atoms should be zero. A value within epsilon of zero is also allowed
in case the data file was generated by another program with finite
numeric precision, in which case the z coord for the atom will be set
to zero.
Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last fix
defined in the input script. It ensures that the z-components of
velocities and forces are zeroed out every timestep. The reason to
make it the last fix is so that any forces added by other fixes will
also be zeroed out.
Many of the example input scripts included in the examples directory
are for 2d models.
.. note::
Some models in LAMMPS treat particles as finite-size spheres, as
opposed to point particles. See the :doc:`atom_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
commands for details. By default, for 2d simulations, such particles
will still be modeled as 3d spheres, not 2d discs (circles), meaning
opposed to point particles. See the :doc:`atom_style sphere
<atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>` commands
for details. By default, for 2d simulations, such particles will
still be modeled as 3d spheres, not 2d discs (circles), meaning
their moment of inertia will be that of a sphere. If you wish to
model them as 2d discs, see the :doc:`set density/disc <set>` command
and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
:doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
commands.
model them as 2d discs, see the :doc:`set density/disc <set>`
command and the *disc* option for the :doc:`fix nve/sphere
<fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
<fix_npt_sphere>` commands.

33
doc/src/Howto_body.rst
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@ -102,8 +102,19 @@ particles of different styles
| :doc:`dump image <dump_image>` | output body particle attributes as an image |
+------------------------------------------------+-----------------------------------------------------+
The pair styles defined for use with specific body styles are listed
in the sections below.
The pair styles currently defined for use with specific body styles
are listed in the sections below.
Note that for all the body styles, if the data file defines a general
triclinic box, then the orientation of the body particle and its
corresponding 6 moments of inertia and other orientation-dependent
values should reflect the fact the body is defined withing a general
triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate
the box to convert it to a restricted triclinic box. This operation
will also rotate the orientation of the body particles. See the
:doc:`Howto triclinic <Howto_triclinic>` doc page for more details.
The sections below highlight the orientation-dependent values specific
to each body style.
----------
@ -154,12 +165,18 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle. The
center-of-mass position of the particle is specified by the x,y,z
values in the *Atoms* section of the data file, as is the total mass
of the body particle.
Note that if the data file defines a general triclinic simulation box,
these sub-particle displacements are orientation-dependent and, as
mentioned above, should reflect the body particle's orientation within
the general triclinic box.
The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
with this body style to compute body/body and body/non-body interactions.
@ -226,6 +243,7 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
@ -270,6 +288,11 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
0 0 0
3.0
Note that if the data file defines a general triclinic simulation box,
these polygon vertex displacements are orientation-dependent and, as
mentioned above, should reflect the body particle's orientation within
the general triclinic box.
The :doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>`
command can be used with this body style to compute body/body
interactions. The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
@ -366,6 +389,7 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
@ -435,6 +459,11 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
The number of edges and faces for a rod or sphere must be listed,
but is ignored.
Note that if the data file defines a general triclinic simulation box,
these polyhedron vertex displacements are orientation-dependent and,
as mentioned above, should reflect the body particle's orientation
within the general triclinic box.
The :doc:`pair_style body/rounded/polhedron
<pair_body_rounded_polyhedron>` command can be used with this body
style to compute body/body interactions. The :doc:`fix

9
doc/src/Howto_bpm.rst
View File

@ -15,7 +15,8 @@ orientation for rotational models. This produces a stress-free initial
state. Furthermore, bonds are allowed to break under large strains,
producing fracture. The examples/bpm directory has sample input scripts
for simulations of the fragmentation of an impacted plate and the
pouring of extended, elastic bodies.
pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
for more general information on the approach and the LAMMPS implementation.
----------
@ -150,3 +151,9 @@ the following are currently compatible with BPM bond styles:
interactions, one will need to switch between different *special_bonds*
settings in the input script. An example is found in
``examples/bpm/impact``.
----------
.. _howto-Clemmer:
**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

2
doc/src/Howto_cmake.rst
View File

@ -349,6 +349,8 @@ Some common LAMMPS specific variables
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_KOKKOS``
- select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
* - ``FFT_SINGLE``
- select whether to use single precision FFTs (default: ``off``)
* - ``WITH_JPEG``

5
doc/src/Howto_granular.rst
View File

@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
To model heat conduction, one must add the temperature and heatflow
atom variables with:
* :doc:`fix property/atom <fix_property_atom>`
a temperature integration fix
* :doc:`fix heat/flow <fix_heat_flow>`
and a heat conduction option defined in both
* :doc:`pair_style granular <pair_granular>`
* :doc:`fix wall/gran <fix_wall_gran>`

7
doc/src/Howto_structured_data.rst
View File

@ -52,8 +52,8 @@ JSON
"ke": 2.4962152903997174569
}
YAML format thermo_style output
===============================
YAML format thermo_style or dump_style output
=============================================
Extracting data from log file
-----------------------------
@ -112,6 +112,9 @@ of that run:
Number of runs: 2
TotEng = -4.62140097780047
Extracting data from dump file
------------------------------
.. versionadded:: 4May2022
YAML format output has been added to multiple commands in LAMMPS,

431
doc/src/Howto_triclinic.rst
View File

@ -2,43 +2,195 @@ Triclinic (non-orthogonal) simulation boxes
===========================================
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The :doc:`boundary <boundary>` command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by **a** = (xhi-xlo,0,0); **b** =
(0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters
particles. The orthogonal box has its "origin" at (xlo,ylo,zlo) and
extends to (xhi,yhi,zhi). Conceptually it is defined by 3 edge
vectors starting from the origin given by **A** = (xhi-xlo,0,0); **B**
= (0,yhi-ylo,0); **C** = (0,0,zhi-zlo). The :doc:`boundary
<boundary>` command sets the boundary conditions for the 6 faces of
the box (periodic, non-periodic, etc). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the
:doc:`thermo_style custom <thermo_style>` command.
is created by one of these commands:
LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
(xz,yz,zhi-zlo). *xy,xz,yz* can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary
vectors. As indicated, **a** must lie on the positive x axis. **b** must
lie in the xy plane, with strictly positive y component. **c** may have
any orientation with strictly positive z component. The requirement
that **a**, **b**, and **c** have strictly positive x, y, and z components,
respectively, ensures that **a**, **b**, and **c** form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.
* :doc:`create_box <create_box>`
* :doc:`read_data <read_data>`
* :doc:`read_restart <read_restart>`
* :doc:`read_dump <read_dump>`
For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge
vectors of a general parallelepiped, where there is no restriction on
**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e.
**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear
rotation of **A**, **B**, and **C** and can be computed as follows:
Internally, LAMMPS defines box size parameters lx,ly,lz where lx =
xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, as
well as lx,ly,lz, can be output via the :doc:`thermo_style custom
<thermo_style>` command. See the :doc:`Howto 2d <Howto_2d>` doc page
for info on how zlo and zhi are defined for 2d simulations.
----------
Triclinic simulation boxes
""""""""""""""""""""""""""
LAMMPS also allows simulations to be performed using triclinic
(non-orthogonal) simulation boxes shaped as a 3d parallelepiped with
triclinic symmetry. For 2d simulations a triclinic simulation box is
effectively a parallelogram; see the :doc:`Howto 2d <Howto_2d>` doc
page for details.
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The :doc:`lattice <lattice>` command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the :doc:`create_atoms
<create_atoms>` command.
A second use is to run Parrinello-Rahman dynamics via the :doc:`fix
npt <fix_nh>` command, which will adjust the xy, xz, yz tilt factors
to compensate for off-diagonal components of the pressure tensor. The
analog for an :doc:`energy minimization <minimize>` is the :doc:`fix
box/relax <fix_box_relax>` command.
A third use is to shear a bulk solid to study the response of the
material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the :doc:`Howto
NEMD <Howto_nemd>` doc page on non-equilibrium MD (NEMD) simulations.
Conceptually, a triclinic parallelepiped is defined with an "origin"
at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** =
(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long
as they are non-zero, distinct, and not co-planar. In addition, they
must define a right-handed system, such that (**A** cross **B**)
points in the direction of **C**. Note that a left-handed system can
be converted to a right-handed system by simply swapping the order of
any pair of the **A**, **B**, **C** vectors.
The 4 commands listed above for defining orthogonal simulation boxes
have triclinic options which allow for specification of the origin and
edge vectors **A**, **B**, **C**. For each command, this can be done
in one of two ways, for what LAMMPS calls a *general* triclinic box or
a *restricted* triclinic box.
A *general* triclinic box is specified by an origin (xlo, ylo, zlo)
and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and
**C** = (cx,cy,cz). So there are 12 parameters in total.
A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its
edge vectors are of the following restricted form: **A** =
(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So
there are 9 parameters in total. Note that the restricted form
requires **A** to be along the x-axis, **B** to be in the xy plane
with a y-component in the +y direction, and **C** to have its
z-component in the +z direction. Note that a restricted triclinic box
is *right-handed* by construction since (**A** cross **B**) points in
the direction of **C**.
The *xy,xz,yz* values can be zero or positive or negative. They are
called "tilt factors" because they are the amount of displacement
applied to edges of faces of an orthogonal box to change it into a
restricted triclinic parallelepiped.
.. note::
Any right-handed general triclinic box (i.e. solid-state crystal
basis vectors) can be rotated in 3d around its origin in order to
conform to the LAMMPS definition of a restricted triclinic box.
See the discussion in the next sub-section about general triclinic
simulation boxes in LAMMPS.
Note that the :doc:`thermo_style custom <thermo_style>` command has
keywords for outputting the various parameters that define the size
and shape of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
For orthogonal boxes there 6 thermo keywords (xlo,ylo,zlo) and
(xhi,yhi,zhi).
For restricted triclinic boxes there are 9 thermo keywords for
(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors.
For general triclinic boxes there are 12 thermo keywords for
(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge
vectors, namely (avecx,avecy,avecz), (bvecx,bvecy,bvecz), and
(cvecx,cvecy,cvecz),
The remainder of this doc page explains (a) how LAMMPS operates with
general triclinic simulation boxes, (b) mathematical transformations
between general and restricted triclinic boxes which may be useful
when creating LAMMPS inputs or interpreting outputs for triclinic
simulations, and (c) how LAMMPS uses tilt factors for restricted
triclinic simulation boxes.
----------
General triclinic simulation boxes in LAMMPS
""""""""""""""""""""""""""""""""""""""""""""
LAMMPS allows specification of general triclinic simulation boxes with
their atoms as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. Likewise it allows output of dump files, data files,
and thermodynamic data (e.g. pressure tensor) in a general triclinic
format.
However internally, LAMMPS only uses restricted triclinic simulation
boxes. This is for parallel efficiency and to formulate partitioning
of the simulation box across processors, neighbor list building, and
inter-processor communication of per-atom data with methods similar to
those used for orthogonal boxes.
This means 4 things which are important to understand:
* Input of a general triclinic system is immediately converted to a
restricted triclinic system.
* If output of per-atom data for a general triclinic system is
requested (e.g. for atom coordinates in a dump file),
conversion from a restricted to general triclinic system is done at
the time of output.
* The conversion of the simulation box and per-atom data from general
triclinic to restricted triclinic (and vice versa) is a 3d rotation
operation around an origin, which is the lower left corner of the
simulation box. This means an input data file for a general
triclinic system should specify all per-atom quantities consistent
with the general triclinic box and its orientation relative to the
standard x,y,z coordinate axes. For example, atom coordinates
should be inside the general triclinic simulation box defined by the
edge vectors **A**, **B**, **C** and its origin. Likewise per-atom
velocities should be in directions consistent with the general
triclinic box orientation. E.g. a velocity vector which will be in
the +x direction once LAMMPS converts from a general to restricted
triclinic box, should be specified in the data file in the direction
of the **A** edge vector. See the :doc:`read_data <read_data>` doc
page for info on all the per-atom vector quantities to which this
rule applies when a data file for a general triclinic box is input.
* If commands such as :doc:`write_data <write_data>` or :doc:`dump
custom <dump>` are used to output general triclinic information, it
is effectively the inverse of the operation described in the
preceding bullet.
* Other LAMMPS commands such as :doc:`region <region>` or
:doc:`velocity <velocity>` or :doc:`set <set>`, operate on a
restricted triclinic system even if a general triclinic system was
defined initially.
This is the list of commands which have general triclinic options:
* :doc:`create_box <create_box>` - define a general triclinic box
* :doc:`create_atoms <create_atoms>` - add atoms to a general triclinic box
* :doc:`lattice <lattice>` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box
* :doc:`read_data <read_data>` - read a data file for a general triclinic system
* :doc:`write_data <write_data>` - write a data file for a general triclinic system
* :doc:`dump atom, dump custom <dump>` - output dump snapshots in general triclinic format
* :doc:`dump_modify triclinic/general <dump_modify>` - select general triclinic format for dump output
* :doc:`thermo_style <thermo_style>` - output the pressure tensor in
general triclinic format
* :doc:`thermo_modify triclinic/general <thermo_modify>` - select general triclinic format for thermo output
* :doc:`read_restart <read_restart>` - read a restart file for a general triclinic system
* :doc:`write_restart <read_restart>` - write a restart file for a general triclinic system
----------
Transformation from general to restricted triclinic boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a
general triclinic simulation box. The equivalent LAMMPS **a**,\
**b**,\ **c** for a restricted triclinic box are a 3d rotation of
**A**, **B**, and **C** and can be computed as follows:
.. math::
@ -55,23 +207,17 @@ rotation of **A**, **B**, and **C** and can be computed as follows:
c_y = & \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\
c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2}
where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
between the vectors described below. Note that by construction,
**a**, **b**, and **c** have strictly positive x, y, and z components, respectively.
If it should happen that
**A**, **B**, and **C** form a left-handed basis, then the above equations
are not valid for **c**\ . In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
where A = \| **A** \| indicates the scalar length of **A**\ . The hat
symbol (\^) indicates the corresponding unit vector. :math:`\beta` and
:math:`\gamma` are angles between the **A**, **B**, **C** vectors
as described below.
For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:
For consistency, the same rotation applied to the triclinic box edge
vectors can also be applied to atom positions, velocities, and other
vector quantities. This can be conveniently achieved by first
converting to fractional coordinates in the general triclinic
coordinates and then converting to coordinates in the restricted
triclinic basis. The transformation is given by the following equation:
.. math::
@ -82,87 +228,24 @@ The transformation is given by the following equation:
\mathbf{A \times B}
\end{pmatrix} \cdot \mathbf{X}
where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis.
where *V* is the volume of the box (same in either basis), **X** is
the fractional vector in the general triclinic basis and **x** is the
resulting vector in the restricted triclinic basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.
----------
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simulation box is created. This happens in one of 3 ways.
If the :doc:`create_box <create_box>` command is used with a region of
style *prism*, then a triclinic box is setup. See the
:doc:`region <region>` command for details. If the
:doc:`read_data <read_data>` command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a triclinic box is setup. See the
:doc:`read_data <read_data>` command for details. Finally, if the
:doc:`read_restart <read_restart>` command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.
Crystallographic general triclinic representation of a simulation box
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the :doc:`fix npt <fix_nh>` or
:doc:`fix deform <fix_deform>` commands. Alternatively, you can use the
:doc:`change_box <change_box>` command to convert a simulation box from
orthogonal to triclinic and vice versa.
As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
:doc:`thermo_style custom <thermo_style>` command.
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the :doc:`fix deform <fix_deform>` or :doc:`fix npt <fix_nh>`
commands.
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` page for further details.
One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
Box flips that may occur using the :doc:`fix deform <fix_deform>` or
:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
option with either of the commands.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped subdomain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Triclinic crystal structures are often defined using three lattice
constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature,
the a, b, and c lattice constants are the scalar lengths of the edge
General triclinic crystal structures are often defined using three
lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the
a, b, and c lattice constants are the scalar lengths of the edge
vectors **a**, **b**, and **c** defined above. The relationship
between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`,
:math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:math:`\gamma`) and the LAMMPS restricted triclinic box sizes
(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is
as follows:
.. math::
@ -186,15 +269,19 @@ The inverse relationship can be written as follows:
The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
:math:`\gamma` can be printed out or accessed by computes using the
:doc:`thermo_style custom <thermo_style>` keywords
*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*,
respectively.
:doc:`thermo_style custom <thermo_style>` keywords *cella*, *cellb*,
*cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively.
----------
Output of restricted and general triclinic boxes in a dump file
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
As discussed on the :doc:`dump <dump>` command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
BOUNDS for a snapshot is written to a dump file for a restricted
triclinic box, an orthogonal bounding box which encloses the triclinic
simulation box is output, along with the 3 tilt factors (xy, xz, yz) of
the restricted triclinic box, formatted as follows:
.. parsed-literal::
@ -204,7 +291,7 @@ box, formatted as follows:
zlo_bound zhi_bound yz
This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
calculated from the 9 restricted triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
.. parsed-literal::
@ -217,22 +304,66 @@ calculated from the 9 triclinic box parameters
zhi_bound = zhi
These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
back into the restricted triclinic box parameters, e.g. xlo =
xlo_bound - MIN(0.0,xy,xz,xy+xz).
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The :doc:`lattice <lattice>` command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
:doc:`create_atoms <create_atoms>` command.
----------
A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt <fix_nh>` command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analog for an :doc:`energy minimization <minimize>` is
the :doc:`fix box/relax <fix_box_relax>` command.
Periodicity and tilt factors for triclinic simulation boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
A third use is to shear a bulk solid to study the response of the
material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in y or z if you wish to
enforce a shift in coordinates due to periodic boundary conditions
across the y or z boundaries. See the doc page for the :doc:`boundary
<boundary>` command for an explanation of shifted coordinates for
restricted triclinic boxes which are periodic.
Some commands that work with triclinic boxes, e.g. the :doc:`fix
deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require
periodicity or non-shrink-wrap boundary conditions in specific
dimensions. See the command doc pages for details.
A restricted triclinic box can be defined with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to use of the :doc:`fix npt
<fix_nh>` or :doc:`fix deform <fix_deform>` commands. Alternatively,
you can use the :doc:`change_box <change_box>` command to convert a
simulation box from orthogonal to restricted triclinic and vice versa.
.. note::
Highly tilted restricted triclinic simulation boxes can be
computationally inefficient. This is due to the large volume of
communication needed to acquire ghost atoms around a processor's
irregular-shaped subdomain. For extreme values of tilt, LAMMPS may
also lose atoms and generate an error.
LAMMPS will issue a warning if you define a restricted triclinic box
with a tilt factor which skews the box more than half the distance of
the parallel box length, which is the first dimension in the tilt
factor (e.g. x for xz).
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor should be between -5 and 5 to avoid the warning.
Similarly, both xz and yz should be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that these are not limitations, since if the
maximum tilt factor is 5 (as in this example), then simulations boxes
and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are
all geometrically equivalent.
If the box tilt exceeds this limit during a dynamics run (e.g. due to
the :doc:`fix deform <fix_deform>` command), then by default the box
is "flipped" to an equivalent shape with a tilt factor within the
warning bounds, and the run continues. See the :doc:`fix deform
<fix_deform>` page for further details. Box flips that would normally
occur using the :doc:`fix deform <fix_deform>` or :doc:`fix npt
<fix_nh>` commands can be suppressed using the *flip no* option with
either of the commands.
One exception to box flipping is if the first dimension in the tilt
factor (e.g. x for xy) is non-periodic. In that case, the limits on
the tilt factor are not enforced, since flipping the box in that
dimension would not change the atom positions due to non-periodicity.
In this mode, if the system tilts to large angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.

25
doc/src/Howto_type_labels.rst
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@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
A recent addition to LAMMPS is the option to use strings - referred to
as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
type labels can make inputs more readable and generic (i.e. usable
through the :doc:`include command <include>` for different systems with
different numerical values assigned to types. This generality also
applies to other inputs like data files read by :doc:`read_data
<read_data>` or molecule template files read by the :doc:`molecule
<molecule>` command. A discussion of the current type label support can
be found in :ref:`(Gissinger) <Typelabel24>`. See below for a list of
other commands that can use type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.
-----------
.. _Typelabel24:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

2
doc/src/Intro_citing.rst
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@ -47,6 +47,8 @@ In addition there are DOIs generated for individual stable releases:
- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 <https://dx.doi.org/10.5281/zenodo.6386596>`_
- 23 June 2022 version: `DOI:10.5281/zenodo.10806836 <https://doi.org/10.5281/zenodo.10806836>`_
- 2 August 2023 version: `DOI:10.5281/zenodo.10806852 <https://doi.org/10.5281/zenodo.10806852>`_
Home page
^^^^^^^^^

4
doc/src/Intro_features.rst
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@ -29,7 +29,7 @@ General features
* spatial decomposition of simulation domain for MPI parallelism
* particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
* GPLv2 licensed open-source distribution
* highly portable C++-11
* highly portable C++-11 (optional packages may require C++17)
* modular code with most functionality in optional packages
* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
* other libraries are optional and only required for specific packages
@ -81,7 +81,7 @@ commands)
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
* charged pairwise potentials: Coulombic, point-dipole
* many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN
* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP
* interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`

12
doc/src/Library_objects.rst
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@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
-----------------------
@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_set_string_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_set_internal_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_variable_info
:project: progguide

6
doc/src/Library_properties.rst
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@ -13,6 +13,7 @@ This section documents the following functions:
- :cpp:func:`lammps_extract_setting`
- :cpp:func:`lammps_extract_global_datatype`
- :cpp:func:`lammps_extract_global`
- :cpp:func:`lammps_map_atom`
--------------------
@ -120,3 +121,8 @@ subdomains and processors.
.. doxygenfunction:: lammps_extract_global
:project: progguide
-----------------------
.. doxygenfunction:: lammps_map_atom
:project: progguide

33
doc/src/Modify_style.rst
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@ -96,6 +96,39 @@ list all non-conforming lines. By adding the `-f` flag to the command
line, they will modify the flagged files to try to remove the detected
issues.
Constants (strongly preferred)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Global or per-file constants should be declared as `static constexpr`
variables rather than via the pre-processor with `#define`. The name of
constants should be all uppercase. This has multiple advantages:
- constants are easily identified as such by their all upper case name
- rather than a pure text substitution during pre-processing, `constexpr
variables` have a type associated with them and are processed later in
the parsing process where the syntax checks and type specific
processing (e.g. via overloads) can be applied to them.
- compilers can emit a warning if the constant is not used and thus can
be removed (we regularly check for and remove dead code like this)
- there are no unexpected substitutions and thus confusing syntax errors
when compiling leading to, for instance, conflicts so that LAMMPS
cannot be compiled with certain combinations of packages (this *has*
happened multiple times in the past).
Pre-processor defines should be limited to macros (but consider C++
templates) and conditional compilation. If a per-processor define must
be used, it should be defined at the top of the .cpp file after the
include statements and at all cost it should be avoided to put them into
header files.
Some sets of commonly used constants are provided in the ``MathConst``
and ``EwaldConst`` namespaces and implemented in the files
``math_const.h`` and ``ewald_const.h``, respectively.
There are always exceptions, special cases, and legacy code in LAMMPS,
so please contact the LAMMPS developers if you are not sure.
Placement of braces (strongly preferred)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

52
doc/src/Packages_details.rst
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@ -52,6 +52,7 @@ page gives those details.
* :ref:`DRUDE <PKG-DRUDE>`
* :ref:`EFF <PKG-EFF>`
* :ref:`ELECTRODE <PKG-ELECTRODE>`
* :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
* :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
* :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
* :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@ -84,6 +85,7 @@ page gives those details.
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`ML-SNAP <PKG-ML-SNAP>`
* :ref:`ML-UF3 <PKG-ML-UF3>`
* :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>`
@ -404,6 +406,7 @@ and :ref:`ASPHERE <PKG-ASPHERE>` packages are installed.
* :doc:`bond_style oxdna2/\* <bond_oxdna>`
* :doc:`bond_style oxrna2/\* <bond_oxdna>`
* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
* examples/PACKAGES/cgdna
----------
@ -677,7 +680,12 @@ DPD-BASIC package
Pair styles for the basic dissipative particle dynamics (DPD) method
and DPD thermostatting.
**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP)
Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
includes smeared charges for coulomb interactions and thus requires the
:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
Coulomb part of the interactions.
**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
**Supporting info:**
@ -686,6 +694,7 @@ and DPD thermostatting.
* :doc:`pair_style dpd/tstat <pair_dpd>`
* :doc:`pair_style dpd/ext <pair_dpd_ext>`
* :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
* examples/PACKAGES/dpd-basic
----------
@ -887,6 +896,22 @@ This package has :ref:`specific installation instructions <electrode>` on the
----------
.. _PKG-EXTRA-COMMAND:
EXTRA-COMMAND package
---------------------
**Contents:**
Additional command styles that are less commonly used.
**Supporting info:**
* src/EXTRA-COMMAND: filenames -> commands
* :doc:`general commands <Commands_all>`
----------
.. _PKG-EXTRA-COMPUTE:
EXTRA-COMPUTE package
@ -1926,6 +1951,31 @@ computes which analyze attributes of the potential.
----------
.. _PKG-ML-UF3:
ML-UF3 package
--------------
**Contents:**
A pair style for the ultra-fast force field potentials (UF3). UF3 is a
methodology for deriving a highly accurate classical potential which is
fast to evaluate and is fitted to a large archives of quantum mechanical
(DFT) data. The use of b-spline basis set in UF3 enables the rapid
evaluation of 2-body and 3-body interactions.
**Authors:** Ajinkya C Hire (University of Florida),
Hendrik Krass (University of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (University of Florida)
**Supporting info:**
* src/ML-UF3: filenames -> commands
* :doc:`pair_style uf3 <pair_uf3>`
* examples/uf3
* https://github.com/uf3/uf3
.. _PKG-MOFFF:
MOFFF package

10
doc/src/Packages_list.rst
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@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
- :doc:`fix electrode/conp <fix_electrode>`
- PACKAGES/electrode
- no
* - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
- additional command styles
- :doc:`general commands <Commands_all>`
- n/a
- no
* - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
- additional compute styles
- :doc:`compute <compute>`
@ -318,6 +323,11 @@ whether an extra library is needed to build and use the package:
- :doc:`pair_style snap <pair_snap>`
- snap
- no
* - :ref:`ML-UF3 <PKG-ML-UF3>`
- quantum-fitted ultra fast potentials
- :doc:`pair_style uf3 <pair_uf3>`
- PACKAGES/uf3
- no
* - :ref:`MOFFF <PKG-MOFFF>`
- styles for `MOF-FF <MOFplus_>`_ force field
- :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`

15
doc/src/Python_scatter.rst
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@ -56,6 +56,19 @@ like this:
x[n3-1] = z coord of atom with ID natoms
lmp.scatter_atoms("x", 1, 3, x)
The coordinates can also be provided as arguments to the initializer of x:
.. code-block:: python
from ctypes import c_double
natoms = 2
n3 = 3*natoms
# init in constructor
x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0)
lmp.scatter_atoms("x", 1, 3, x)
# or using a list
coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0]
x = (c_double*len(coords))(*coords)
Alternatively, you can just change values in the vector returned by
the gather methods, since they are also ctypes vectors.

58
doc/src/Speed_kokkos.rst
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@ -20,11 +20,28 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
(Sandia). For more information on developing using Kokkos abstractions
see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
Kokkos currently provides support for 4 modes of execution (per MPI
.. note::
The Kokkos library is under active development and tracking the
availability of accelerator hardware, so is the KOKKOS package in
LAMMPS. This means that only a certain range of versions of the
Kokkos library are compatible with the KOKKOS package of a certain
range of LAMMPS versions. For that reason LAMMPS comes with a
bundled version of the Kokkos library that has been validated on
multiple platforms and may contain selected back-ported bug fixes
from upstream Kokkos versions. While it is possible to build LAMMPS
with an external version of Kokkos, it is untested and may result in
incorrect execution or crashes.
Kokkos currently provides full support for 4 modes of execution (per MPI
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA GPUs) and
HIP (for AMD GPUs). Additional modes (e.g. OpenMP target, Intel data
center GPUs) are under development. You choose the mode at build time
to produce an executable compatible with a specific hardware.
The following compatibility notes have been last updated for LAMMPS
version 23 November 2023 and Kokkos version 4.2.
.. admonition:: C++17 support
:class: note
@ -63,13 +80,13 @@ produce an executable compatible with a specific hardware.
LAMMPS command line or by using the command :doc:`package kokkos
gpu/aware off <package>` in the input file.
.. admonition:: AMD GPU support
.. admonition:: Intel Data Center GPU support
:class: note
To build with Kokkos the HIPCC compiler from the AMD ROCm software
version 3.5 or later is required. Supporting this Kokkos mode in
LAMMPS is still work in progress. Please contact the LAMMPS developers
if you run into problems.
Support for Kokkos with Intel Data Center GPU accelerators (formerly
known under the code name "Ponte Vecchio") in LAMMPS is still a work
in progress. Only a subset of the functionality works correctly.
Please contact the LAMMPS developers if you run into problems.
Building LAMMPS with the KOKKOS package
"""""""""""""""""""""""""""""""""""""""
@ -292,6 +309,10 @@ one or more nodes, each with two GPUs:
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
.. note::
The default binsize for :doc:`atom sorting <atom_modify>` on GPUs
@ -302,9 +323,15 @@ one or more nodes, each with two GPUs:
frequent sorting than default (e.g. sorting every 100 time steps
instead of 1000) may improve performance.
.. code-block:: bash
.. note::
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
When running on GPUs with many MPI ranks (tens of thousands and
more), the creation of the atom map (required for molecular systems)
on the GPU can slow down significantly or run out of GPU memory and
thus slow down the whole calculation or cause a crash. You can use
the "-pk kokkos atom/map no" :doc:`command-line switch <Run_options>`
of the :doc:`package kokkos atom/map no <package>` command to create
the atom map on the CPU instead.
.. note::
@ -420,11 +447,18 @@ Generally speaking, the following rules of thumb apply:
of using single or mixed precision with the GPU package depends
significantly on the hardware in use and the simulated system and pair
style.
* When running on Intel hardware, KOKKOS is not as fast as
* When running on Intel Phi hardware, KOKKOS is not as fast as
the INTEL package, which is optimized for x86 hardware (not just
from Intel) and compilation with the Intel compilers. The INTEL
package also can increase the vector length of vector instructions
by switching to single or mixed precision mode.
* The KOKKOS package by default assumes that you are using exactly one
MPI rank per GPU. When trying to use multiple MPI ranks per GPU it is
mandatory to enable `CUDA Multi-Process Service (MPS)
<https://docs.nvidia.com/deploy/mps/index.html>`_ to get good
performance. In this case it is better to not use all available
MPI ranks in order to avoid competing with the MPS daemon for
CPU resources.
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS website for performance of the KOKKOS package on different

70
doc/src/Tools.rst
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@ -90,7 +90,7 @@ Miscellaneous tools
* :ref:`LAMMPS coding standards <coding_standard>`
* :ref:`emacs <emacs>`
* :ref:`i-pi <ipi>`
* :ref:`i-PI <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS GUI <lammps_gui>`
@ -376,21 +376,40 @@ See README file in the tools/fep directory.
.. _ipi:
i-pi tool
i-PI tool
-------------------
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the :doc:`fix ipi <fix_ipi>` command to perform
path-integral molecular dynamics (PIMD).
.. versionchanged:: TBD
The tools/i-pi directory used to contain a bundled version of the i-PI
software package for use with LAMMPS. This version, however, was
removed in 06/2024.
The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.
See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
:doc:`fix ipi <fix_ipi>` page for further details on running PIMD
calculations with LAMMPS.
i-PI is now available via PyPi using the pip package manager at:
https://pypi.org/project/ipi/
Here are the commands to set up a virtual environment and install
i-PI into it with all its dependencies.
.. code-block:: sh
python -m venv ipienv
source ipienv/bin/activate
pip install --upgrade pip
pip install ipi
To install the development version from GitHub, please use:
.. code-block:: sh
pip install git+https://github.com/i-pi/i-pi.git
For further information, please consult the [i-PI home
page](https://ipi-code.org).
----------
@ -709,8 +728,8 @@ CMake is required.
The LAMMPS GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@ -752,22 +771,23 @@ if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred
unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
It should be possible to build the LAMMPS GUI as a standalone
compilation (e.g. when LAMMPS has been compiled with traditional make),
then the CMake configuration needs to be told where to find the LAMMPS
compilation (e.g. when LAMMPS has been compiled with traditional make).
Then the CMake configuration needs to be told where to find the LAMMPS
headers and the LAMMPS library, via ``-D
LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a
build folder with the LAMMPS library from that path, but it can also be
set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader library that will load
possible to compile the GUI with a plugin loader that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be updated LAMMPS without having
to recompile the GUI. The ABI of the LAMMPS C-library interface is very
stable and generally backward compatible. This feature is enabled by
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
advantage that the LAMMPS library can be built from updated or modified
LAMMPS source without having to recompile the GUI. The ABI of the
LAMMPS C-library interface is very stable and generally backward
compatible. This feature is enabled by setting
``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
@ -779,8 +799,8 @@ macOS
"""""
When building on macOS, the build procedure will try to manufacture a
drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
drag-n-drop installer, ``LAMMPS-macOS-multiarch.dmg``, when using the
'dmg' target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
To build multi-arch executables that will run on both, arm64 and x86_64
architectures natively, it is necessary to set the CMake variable ``-D
@ -820,11 +840,11 @@ and LAMMPS GUI can be launched from anywhere from the command line.
The standard CMake build procedure can be applied and the
``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
command will automatically include a suitable CMake toolset file (the
regular cmake command can be used after that). After building the
libraries and executables, you can build the target 'zip'
(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
to stage all installed files into a LAMMPS_GUI folder and then
run a script to copy all required dependencies, some other files,
regular cmake command can be used after that to modify the configuration
settings, if needed). After building the libraries and executables,
you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
or ``make zip`` to stage all installed files into a LAMMPS_GUI folder
and then run a script to copy all required dependencies, some other files,
and create a zip file from it.
Linux

4
doc/src/angle_charmm.rst
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@ -70,7 +70,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

80
doc/src/angle_cosine_squared_restricted.rst Normal file
View File

@ -0,0 +1,80 @@
.. index:: angle_style cosine/squared/restricted
.. index:: angle_style cosine/squared/restricted/omp
angle_style cosine/squared/restricted command
=============================================
Accelerator Variants: *cosine/squared/restricted/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/squared/restricted
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/squared/restricted
angle_coeff 2*4 75.0 100.0
Description
"""""""""""
.. versionadded:: 17Apr2024
The *cosine/squared/restricted* angle style uses the potential
.. math::
E = K [\cos(\theta) - \cos(\theta_0)]^2 / \sin^2(\theta)
, which is commonly used in the MARTINI force field,
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
is a prefactor. Note that the usual 1/2 factor is included in :math:`K`.
See :ref:`(Bulacu) <restricted-Bulacu>` for a description of the restricted angle for the MARTINI force field.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _restricted-Bulacu:
**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
(2013).

2
doc/src/angle_lepton.rst
View File

@ -51,7 +51,7 @@ angle coefficient. For example `"200.0*theta^2"` represents a
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
.. versionchanged:: TBD
.. versionchanged:: 7Feb2024
By default the potential energy U is shifted so that the value U is 0.0
for $theta = theta_0$. This is equivalent to using the optional keyword

3
doc/src/angle_style.rst
View File

@ -10,7 +10,7 @@ Syntax
angle_style style
* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cosine/squared/restricted* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
Examples
""""""""
@ -84,6 +84,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`cosine/shift <angle_cosine_shift>` - angle cosine with a shift
* :doc:`cosine/shift/exp <angle_cosine_shift_exp>` - cosine with shift and exponential term in spring constant
* :doc:`cosine/squared <angle_cosine_squared>` - angle with cosine squared term
* :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` - angle with restricted cosine squared term
* :doc:`cross <angle_cross>` - cross term coupling angle and bond lengths
* :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
* :doc:`fourier <angle_fourier>` - angle with multiple cosine terms

625
doc/src/atom_style.rst
View File

@ -49,252 +49,229 @@ Examples
Description
"""""""""""
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
command.
The *atom_style* command selects which per-atom attributes are
associated with atoms in a LAMMPS simulation and thus stored and
communicated with those atoms as well as read from and stored in data
and restart files. Different models (e.g. :doc:`pair styles
<pair_style>`) require access to specific per-atom attributes and thus
require a specific atom style. For example, to compute Coulomb
interactions, the atom must have a "charge" (aka "q") attribute.
A number of distinct atom styles exist that combine attributes. Some
atom styles are a superset of other atom styles. Further attributes
may be added to atoms either via using a hybrid style which provides a
union of the attributes of the sub-styles, or via the :doc:`fix
property/atom <fix_property_atom>` command. The *atom_style* command
must be used before a simulation is setup via a :doc:`read_data
<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
<create_box>` command.
.. note::
Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Many of the atom styles discussed here are only enabled if LAMMPS was
built with a specific package, as listed below in the Restrictions
section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style *bond*, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
Once a style is selected and the simulation box defined, it cannot be
changed but only augmented with the :doc:`fix property/atom
<fix_property_atom>` command. So one should select an atom style
general enough to encompass all attributes required. E.g. with atom
style *bond*, it is not possible to define angles and use angle styles.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the :doc:`read_data <read_data>` command.
It is OK to use a style more general than needed, though it may be
slightly inefficient because it will allocate and communicate
additional unused data.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
Atom style attributes
"""""""""""""""""""""
The atom style *atomic* has the minimum subset of per-atom attributes
and is also the default setting. It encompasses the following per-atom
attributes (name of the vector or array in the :doc:`Atom class
<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
position (x), velocities (v), forces (f), image flags (image), group
membership (mask). Since all atom styles are a superset of atom style
*atomic*\ , they all include these attributes.
This table lists all the available atom styles, which attributes they
provide, which :doc:`package <Packages>` is required to use them, and
what the typical applications are that use them. See the
:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
:doc:`set <set>` commands for info on how to set these various
quantities.
:doc:`set <set>` commands for details on how to set these various
quantities. More information about many of the styles is provided in
the Additional Information section below.
+----------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+----------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+----------------+-----------------------------------------------------+--------------------------------------+
| *atomic* | only the default values | coarse-grain liquids, solids, metals |
+----------------+-----------------------------------------------------+--------------------------------------+
| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
+----------------+-----------------------------------------------------+--------------------------------------+
| *bond* | bonds | bead-spring polymers |
+----------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+----------------+-----------------------------------------------------+--------------------------------------+
| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
+----------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *dpd* | internal temperature and internal energies | DPD particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *edpd* | temperature and heat capacity | eDPD particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+----------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *full* | molecular + charge | bio-molecules |
+----------------+-----------------------------------------------------+--------------------------------------+
| *line* | end points, angular velocity | rigid bodies |
+----------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+----------------+-----------------------------------------------------+--------------------------------------+
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
+----------------+-----------------------------------------------------+--------------------------------------+
| *peri* | mass, volume | mesoscopic Peridynamic models |
+----------------+-----------------------------------------------------+--------------------------------------+
| *rheo* | rho, status | solid and fluid RHEO particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *rheo/thermal* | rho, status, temperature | RHEO particles with temperature |
+----------------+-----------------------------------------------------+--------------------------------------+
| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *sph* | rho, esph, cv | SPH particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *sphere* | diameter, mass, angular velocity | granular models |
+----------------+-----------------------------------------------------+--------------------------------------+
| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
+----------------+-----------------------------------------------------+--------------------------------------+
| *spin* | magnetic moment | system with magnetic particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *tdpd* | chemical concentration | tDPD particles |
+----------------+-----------------------------------------------------+--------------------------------------+
| *template* | template index, template atom | small molecules with fixed topology |
+----------------+-----------------------------------------------------+--------------------------------------+
| *tri* | corner points, angular momentum | rigid bodies |
+----------------+-----------------------------------------------------+--------------------------------------+
| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
+----------------+-----------------------------------------------------+--------------------------------------+
.. list-table::
:header-rows: 1
:widths: auto
* - Atom style
- Attributes
- Required package
- Applications
* - *amoeba*
- *full* + "1-5 special neighbor data"
- :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA/HIPPO force fields
* - *angle*
- *bond* + "angle data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers with stiffness
* - *atomic*
- tag, type, x, v, f, image, mask
-
- atomic liquids, solids, metals
* - *body*
- *atomic* + radius, rmass, angmom, torque, body
- :ref:`BODY <PKG-BODY>`
- arbitrary bodies, see :doc:`body howto <Howto_body>`
* - *bond*
- *atomic* + molecule, nspecial, special + "bond data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers
* - *bpm/sphere*
- *bond* + radius, rmass, omega, torque, quat
- :ref:`BPM <PKG-BPM>`
- granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
* - *charge*
- *atomic* + q
-
- atomic systems with charges
* - *dielectric*
- *full* + mu, area, ed, em, epsilon, curvature, q_scaled
- :ref:`DIELECTRIC <PKG-DIELECTRIC>`
- systems with surface polarization
* - *dipole*
- *charge* + mu
- :ref:`DIPOLE <PKG-DIPOLE>`
- atomic systems with charges and point dipoles
* - *dpd*
- *atomic* + rho + "reactive DPD data"
- :ref:`DPD-REACT <PKG-DPD-REACT>`
- reactive DPD
* - *edpd*
- *atomic* + "eDPD data"
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Energy conservative DPD (eDPD)
* - *electron*
- *charge* + espin, eradius, ervel, erforce
- :ref:`EFF <PKG-EFF>`
- Electron force field systems
* - *ellipsoid*
- *atomic* + rmass, angmom, torque, ellipsoid
-
- aspherical particles
* - *full*
- *molecular* + q
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular force fields
* - *line*
- *atomic* + molecule, radius, rmass, omega, torque, line
-
- 2-d rigid body particles
* - *mdpd*
- *atomic* + rho, drho, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Many-body DPD (mDPD)
* - *molecular*
- *angle* + "dihedral and improper data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- apolar and uncharged molecules
* - *oxdna*
- *atomic* + id5p
- :ref:`CG-DNA <PKG-CG-DNA>`
- coarse-grained DNA and RNA models
* - *peri*
- *atomic* + rmass, vfrac, s0, x0
- :ref:`PERI <PKG-PERI>`
- mesoscopic Peridynamics models
* - *smd*
- *atomic* + molecule, radius, rmass + "smd data"
- :ref:`MACHDYN <PKG-MACHDYN>`
- Smooth Mach Dynamics models
* - *rheo*
- *atomic* + rho, status
- :ref:`RHEO <PKG-RHEO>`
- solid and fluid RHEO particles
* - *rheo/thermal*
- *atomic* + rho, status, temperature
- :ref:`RHEO <PKG-RHEO>`
- RHEO particles with temperature
* - *sph*
- *atomic* + "sph data"
- :ref:`SPH <PKG-SPH>`
- Smoothed particle hydrodynamics models
* - *sphere*
- *atomic* + radius, rmass, omega, torque
-
- finite size spherical particles, e.g. granular models
* - *spin*
- *atomic* + "magnetic moment data"
- :ref:`SPIN <PKG-SPIN>`
- magnetic particles
* - *tdpd*
- *atomic* + cc, cc_flux, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Transport DPD (tDPD)
* - *template*
- *atomic* + molecule, molindex, molatom
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular systems where attributes are taken from :doc:`molecule files <molecule>`
* - *tri*
- *sphere* + molecule, angmom, tri
-
- 3-d triangulated rigid body LJ particles
* - *wavepacket*
- *charge* + "wavepacket data"
- :ref:`AWPMD <PKG-AWPMD>`
- Antisymmetrized wave packet MD
.. note::
It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the :doc:`fix property/atom
<fix_property_atom>` command. This command also allows new custom
attributes consisting of extra integer or floating-point values to
be added to atoms. See the :doc:`fix property/atom
<fix_property_atom>` page for examples of cases where this is
useful and details on how to initialize, access, and output the
custom values.
It is possible to add some attributes, such as a molecule ID and
charge, to atom styles that do not have them built in using the
:doc:`fix property/atom <fix_property_atom>` command. This command
also allows new custom-named attributes consisting of extra integer
or floating-point values or vectors to be added to atoms. See the
:doc:`fix property/atom <fix_property_atom>` page for examples of
cases where this is useful and details on how to initialize,
access, and output these custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
*tri*, and *body* styles, which define finite-size particles. See the
:doc:`Howto spherical <Howto_spherical>` page for an overview of using
finite-size particle models with LAMMPS.
----------
All of the point-particle styles assign mass to particles on a
per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
Particle size and mass
""""""""""""""""""""""
For the *sphere* and *bpm/sphere* styles, the particles are spheres
and each stores a per-particle diameter and mass. If the diameter >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by use of the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
spheres can be effectively treated as 2d discs for a 2d simulation if
desired. See also the :doc:`set density/disc <set>` command. These
styles take an optional 0 or 1 argument. A value of 0 means the
radius of each sphere is constant for the duration of the simulation.
A value of 1 means the radii may vary dynamically during the simulation,
e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
All of the atom styles define point particles unless they (1) define
finite-size spherical particles via the *radius* attribute, or (2)
define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
*line*, and *tri* styles). Most of these styles can also be used with
mixtures of point and finite-size particles.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
Note that the *radius* property may need to be provided as a
*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
files <read_data>`). See the :doc:`Howto spherical <Howto_spherical>`
page for an overview of using finite-size spherical and aspherical
particle models with LAMMPS.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
Unless an atom style defines the per-atom *rmass* attribute, particle
masses are defined on a per-type basis, using the :doc:`mass <mass>`
command. This means each particle's mass is indexed by its atom
*type*.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use atom_style hybrid sphere dipole, which will assign both a
diameter and dipole moment to each particle.
A few styles define the per-atom *rmass* attribute which can also be
added using the :doc:`fix property/atom <fix_property_atom>` command.
In this case each particle stores its own mass. Atom styles that have
a per-atom rmass may define it indirectly through setting particle
diameter and density on a per-particle basis. If both per-type mass
and per-atom *rmass* are defined (e.g. in a hybrid style), the
per-atom mass will take precedence in any operation which which works
with both flavors of mass.
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
----------
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *bpm/sphere* style is part of the BPM package.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand. Note that this style is part of the CG-DNA package.
The *dpd* style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the DPD-REACT package, and is not for use with
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
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 *sph* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (esph), and heat capacity
(cv).
The *smd* style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetrating each other.
For the *spin* style, a magnetic spin is associated to each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *wavepacket* style is similar to *electron*, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical *etag* values.
For the *line* style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the *tri* style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
*template* style instead of the *bond*, *angle*, *molecular* styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
Additional information about specific atom styles
"""""""""""""""""""""""""""""""""""""""""""""""""
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -313,6 +290,149 @@ Note that there may be additional arguments required along with the
*bstyle* specification, in the atom_style body command. These
arguments are described on the :doc:`Howto body <Howto_body>` doc page.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a
boundary element between two regions of different dielectric
constant. For interface particles, in addition to the properties
associated with atom_style full, each particle also should be assigned
a unit dipole vector (mu) representing the direction of the induced
dipole moment at each interface particle, an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a
mean local curvature (curv). Physical particles must be assigned
these values, as well, but only their local dielectric constants will
be used; see documentation for associated :doc:`pair styles
<pair_dielectric>` and :doc:`fixes <fix_polarize>`. The distinction
between the physical and interface particles is only meaningful when
:doc:`fix polarize <fix_polarize>` commands are applied to the
interface particles. This style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole vector mu is defined for each
point particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use the command `atom_style hybrid sphere dipole`, which will
assign both a diameter and dipole moment to each particle. This also
requires using an integrator with a "/sphere" suffix like :doc:`fix
nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
and the "update dipole" or "update dlm" parameters to the fix
commands.
The *dpd* style is for reactive dissipative particle dynamics (DPD)
particles. Note that it is part of the DPD-REACT package, and is not
required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
commands, which only require the attributes from atom_style *atomic*.
Atom_style *dpd* extends DPD particle 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).
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the *ellipsoid* style, particles can be ellipsoids which each
stores a shape vector with the 3 diameters of the ellipsoid and a
quaternion 4-vector with its orientation. Each particle stores a flag
in the ellipsoid vector which indicates whether it is an ellipsoid (1)
or a point particle (0).
For the *line* style, particles can be are idealized line segments
which store a per-particle mass and length and orientation (i.e. the
end points of the line segment). Each particle stores a flag in the
line vector which indicates whether it is a line segment (1) or a
point particle (0).
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 *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *smd* style is for Smooth Particle Mach dynamics. Both fluids and
solids can be modeled. Particles store the mass and volume of an
integration point, a kernel diameter used for calculating the field
variables (e.g. stress and deformation) and a contact radius for
calculating repulsive forces which prevent individual physical bodies
from penetrating each other.
The *sph* style is for smoothed particle hydrodynamics (SPH) particles
which store a density (rho), energy (esph), and heat capacity (cv).
For the *spin* style, a magnetic spin is associated with each atom.
Those spins have a norm (their magnetic moment) and a direction.
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 *wavepacket* style is similar to the *electron* style, but the
electrons may consist of several Gaussian wave packets, summed up with
coefficients cs= (cs_re,cs_im). Each of the wave packets is treated
as a separate particle in LAMMPS, wave packets belonging to the same
electron must have identical *etag* values.
The *sphere* and *bpm/sphere* styles allow particles to be either point
particles or finite-size particles. If the *radius* attribute is >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by using the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. These styles also
take an optional 0 or 1 argument. A value of 0 means the radius of
each sphere is constant for the duration of the simulation (this is
the default). A value of 1 means the radii may vary dynamically
during the simulation, e.g. due to use of the :doc:`fix adapt
<fix_adapt>` command.
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms only
store a template index and template atom to identify which molecule and
which atom-within-the-molecule they represent. Using the *template*
style instead of the *bond*, *angle*, *molecular* styles can save memory
for systems comprised of a large number of small molecules, all of a
single type (or small number of types). See the paper by Grime and
Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
advantageous for large-scale coarse-grained systems. The
``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
For the *tri* style, particles can be planar triangles which each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle). Each particle stores a flag in the tri
vector which indicates whether it is a triangle (1) or a point
particle (0).
----------
Typically, simulations require only a single (non-hybrid) atom style.
@ -333,8 +453,9 @@ When using the *hybrid* style, you cannot combine the *template* style
with another molecular style that stores bond, angle, etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see the :doc:`Modify <Modify>` doc page.
LAMMPS can be extended with new atom styles as well as new body styles;
see the corresponding manual page on :doc:`modifying & extending LAMMPS
<Modify_atom>`.
----------
@ -350,54 +471,20 @@ This command cannot be used after the simulation box is defined by a
Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :doc:`Build package
<Build_package>` page for more info.
The *amoeba* style is part of the AMOEBA package.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
The *line* and *tri* styles are part of the ASPHERE package.
The *body* style is part of the BODY package.
The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *oxdna* style is part of the CG-DNA package for coarse-grained
simulation of DNA and RNA.
The *electron* style is part of the EFF package for :doc:`electronic
force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
<Build_package>` page for more info. The table above lists which package
is required for individual atom styles.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
Default
"""""""
The default atom style is atomic. If atom_style sphere is used its
default argument is 0.
The default atom style is *atomic*. If atom_style *sphere* or
*bpm/sphere* is used, its default argument is 0.
----------

9
doc/src/bond_hybrid.rst
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@ -1,8 +1,11 @@
.. index:: bond_style hybrid
.. index:: bond_style hybrid/kk
bond_style hybrid command
=========================
Accelerator Variants: *hybrid/kk*
Syntax
""""""
@ -15,7 +18,7 @@ Syntax
Examples
""""""""
.. code-block: LAMMPS
.. code-block:: LAMMPS
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
@ -60,6 +63,10 @@ bond types.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

2
doc/src/bond_lepton.rst
View File

@ -50,7 +50,7 @@ constant *K* of 200.0 energy units:
U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
.. versionchanged:: TBD
.. versionchanged:: 7Feb2024
By default the potential energy U is shifted so that he value U is 0.0
for $r = r_0$. This is equivalent to using the optional keyword

122
doc/src/bond_oxdna.rst
View File

@ -27,6 +27,7 @@ Examples
.. code-block:: LAMMPS
# LJ units
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
@ -36,6 +37,32 @@ Examples
bond_style oxrna2/fene
bond_coeff * 2.0 0.25 0.76107
bond_style oxdna/fene
bond_coeff * oxdna_lj.cgdna
# Real units
bond_style oxdna/fene
bond_coeff * 11.92337812042065 2.1295 6.409795
bond_style oxdna2/fene
bond_coeff * 11.92337812042065 2.1295 6.4430152
bond_style oxrna2/fene
bond_coeff * 11.92337812042065 2.1295 6.482800913
bond_style oxrna2/fene
bond_coeff * oxrna2_real.cgdna
.. note::
The coefficients in the above examples have to be kept fixed and
cannot be changed without reparameterizing the entire model. They are
provided in forms compatible with both *units lj* and *units real*
(see documentation of :doc:`units <units>`). These can also be read
from a potential file with correct unit style by specifying the name
of the file. Several potential files for each unit style are included
in the ``potentials`` directory of the LAMMPS distribution.
Description
"""""""""""
@ -46,15 +73,14 @@ The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
to define a modified finite extensible nonlinear elastic (FENE)
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of
the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
modelling of DNA/RNA.
The following coefficients must be defined for the bond type via the
:doc:`bond_coeff <bond_coeff>` command as given in the above example, or
in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
in the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* :math:`\epsilon` (energy)
* :math:`\Delta` (distance)
@ -62,41 +88,40 @@ commands:
.. note::
The oxDNA bond style has to be used together with the
corresponding oxDNA pair styles for excluded volume interaction
*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
coaxial stacking interaction *oxdna/coaxstk* as well as
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
:doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
*oxdna2/hbond* and an additional Debye-Hueckel pair style
*oxdna2/dh* have to be defined. The same applies to the oxRNA2
:ref:`(Sulc1) <Sulc01>` styles.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model.
The oxDNA bond style has to be used together with the corresponding
oxDNA pair styles for excluded volume interaction *oxdna/excv* ,
stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial
stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding
interaction *oxdna/hbond* (see also documentation of :doc:`pair_style
oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
*oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.
.. note::
This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna*
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a bond definition
is understood to point towards the 3'-end (5'-end) of the strand.
This bond style has to be used with the *atom_style hybrid bond
ellipsoid oxdna* (see documentation of :doc:`atom_style
<atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
of the nucleotide strand, which is set through the bond topology in
the data file. The first (second) atom in a bond definition is
understood to point towards the 3'-end (5'-end) of the strand.
.. warning::
If data files are produced with :doc:`write_data <write_data>`, then the
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
Otherwise the data files will not have the same 3'-to-5' polarity as the
initial data file. This limitation does not apply to binary restart files
produced with :doc:`write_restart <write_restart>`.
If data files are produced with :doc:`write_data <write_data>`, then
the :doc:`newton <newton>` command should be set to *newton on* or
*newton off on*. Otherwise the data files will not have the same
3'-to-5' polarity as the initial data file. This limitation does not
apply to binary restart files produced with :doc:`write_restart
<write_restart>`.
Example input and data files for DNA and RNA duplexes can be found in
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
setup tool which creates single straight or helical DNA strands, DNA/RNA
duplexes or arrays of DNA/RNA duplexes can be found in
examples/PACKAGES/cgdna/util/.
``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
``.../oxRNA2/``. A simple python setup tool which creates single
straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
duplexes can be found in ``examples/PACKAGES/cgdna/util/``.
Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
this implementation. An updated documentation that contains general information
@ -113,6 +138,39 @@ and for sequence-specific hydrogen-bonding and stacking interactions
----------
Potential file reading
""""""""""""""""""""""
For each style oxdna, oxdna2 and oxrna2, the first parameter argument
can be a filename, and if it is, no further arguments should be
supplied. Therefore the following command:
.. code-block:: LAMMPS
bond_style oxdna/fene
bond_coeff * oxdna_lj.cgdna
will be interpreted as a request to read the (FENE) potential
:ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given
name. The file can define multiple potential parameters for both bonded
and pair interactions, but for the above bonded interactions there must
exist in the file a line of the form:
.. code-block:: LAMMPS
* fene epsilon delta r0
There are sample potential files for each unit style in the
``potentials`` directory of the LAMMPS distribution. The potential file
unit system must align with the units defined via the :doc:`units
<units>` command. For conversion between different *LJ* and *real* unit
systems for oxDNA, the python tool *lj2real.py* located in the
``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
assumes similar file structure to the examples found in
``examples/PACKAGES/cgdna/examples/``.
----------
Restrictions
""""""""""""

54
doc/src/boundary.rst
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@ -42,8 +42,10 @@ commands.
The style *p* means the box is periodic, so that particles interact
across the boundary, and they can exit one end of the box and re-enter
the other end. A periodic dimension can change in size due to
constant pressure boundary conditions or box deformation (see the :doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands). The *p*
style must be applied to both faces of a dimension.
constant pressure boundary conditions or box deformation (see the
:doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands).
The *p* style must be applied to both faces of a dimension. For 2d
simulations the z dimension must be periodic (which is the default).
The styles *f*, *s*, and *m* mean the box is non-periodic, so that
particles do not interact across the boundary and do not move from one
@ -76,28 +78,44 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
LAMMPS also allows use of triclinic (non-orthogonal) simulation boxes.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
description of both general and restricted triclinic boxes and how to
define them. General triclinic boxes (arbitrary edge vectors **A**,
**B**, and **C**) are converted internally to restricted triclinic
boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal
box.
The boundary <boundary> command settings explained above for the 6
faces of an orthogonal box also apply in similar manner to the 6 faces
of a restricted triclinic box (and thus to the corresponding 6 faces
of a general triclinic box), with the following context.
if the second dimension of a tilt factor (e.g. y for xy) is periodic,
then the periodicity is enforced with the tilt factor offset. This
means that for y periodicity a particle which exits the lower y
boundary is displaced in the x-direction by xy before it re-enters the
upper y boundary. And vice versa if a particle exits the upper y
boundary. Likewise the ghost atoms surrounding a particle near the
lower y boundary include images of particles near the upper y-boundary
which are displaced in the x-direction by xy. Similar rules apply for
z-periodicity and the xz and/or yz tilt factors.
If the first dimension of a tilt factor is shrink-wrapped, then the
shrink wrapping is applied to the tilted box face, to encompass the
atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box
are planes tilting in the +y direction as y increases. The position
of these tilted planes are adjusted dynamically to shrink-wrap around
the atoms to determine the xlo and xhi extents of the box.
Restrictions
""""""""""""
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command. See the
:doc:`change_box <change_box>` command for how to change the simulation
box boundaries after it has been defined.
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command
or :doc:`read_restart <read_restart>` command. See the
:doc:`change_box <change_box>` command for how to change the
simulation box boundaries after it has been defined.
For 2d simulations, the z dimension must be periodic.

19
doc/src/compute_adf.rst
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@ -204,8 +204,23 @@ angles per atom satisfying the ADF criteria.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default, the ADF is not computed for distances longer than the
largest force cutoff, since the neighbor list creation will only contain
pairs up to that distance (plus neighbor list skin). If you use outer
cutoffs larger than that, you must use :doc:`neighbor style 'bin' or
'nsq' <neighbor>`.
If you want an ADF for a larger outer cutoff, you can also use the
:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
style zero <pair_zero>` and set the force cutoff to be larger in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary and with pair style zero you are not computing any forces, and
since you are not running dynamics you are not changing the model that
generated the trajectory.
The ADF is not computed for neighbors outside the force cutoff,
since processors (in parallel) don't know about atom coordinates for

2
doc/src/compute_ave_sphere_atom.rst
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@ -102,6 +102,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

2
doc/src/compute_composition_atom.rst
View File

@ -107,6 +107,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

38
doc/src/compute_count_type.rst
View File

@ -12,7 +12,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* count/type = style name of this compute command
* mode = {atom} or {bond} or {angle} or {dihedral} or {improper}
* mode = *atom* or *bond* or *angle* or *dihedral* or *improper*
Examples
""""""""
@ -69,29 +69,42 @@ for each type:
----------
If the {mode} setting is {atom} then the count of atoms for each atom
If the *mode* setting is *atom* then the count of atoms for each atom
type is tallied. Only atoms in the specified group are counted.
If the {mode} setting is {bond} then the count of bonds for each bond
The atom count for each type can be normalized by the total number of
atoms like so:
.. code-block:: LAMMPS
compute typevec all count/type atom # number of atoms of each type
variable normtypes vector c_typevec/atoms # divide by total number of atoms
variable ntypes equal extract_setting(ntypes) # number of atom types
thermo_style custom step v_normtypes[*${ntypes}] # vector variable needs upper limit
Similarly, bond counts can be normalized by the total number of bonds.
The same goes for angles, dihedrals, and impropers (see below).
If the *mode* setting is *bond* then the count of bonds for each bond
type is tallied. Only bonds with both atoms in the specified group
are counted.
For {mode} = {bond}, broken bonds with a bond type of zero are also
For *mode* = *bond*, broken bonds with a bond type of zero are also
counted. The :doc:`bond_style quartic <bond_quartic>` and :doc:`BPM
bond styles <Howto_bpm>` break bonds by doing this. See the :doc:`
Howto broken bonds <Howto_broken_bonds>` doc page for more details.
bond styles <Howto_bpm>` break bonds by doing this. See the
:doc:`Howto broken bonds <Howto_broken_bonds>` doc page for more details.
Note that the group setting is ignored for broken bonds; all broken
bonds in the system are counted.
If the {mode} setting is {angle} then the count of angles for each
If the *mode* setting is *angle* then the count of angles for each
angle type is tallied. Only angles with all 3 atoms in the specified
group are counted.
If the {mode} setting is {dihedral} then the count of dihedrals for
If the *mode* setting is *dihedral* then the count of dihedrals for
each dihedral type is tallied. Only dihedrals with all 4 atoms in the
specified group are counted.
If the {mode} setting is {improper} then the count of impropers for
If the *mode* setting is *improper* then the count of impropers for
each improper type is tallied. Only impropers with all 4 atoms in the
specified group are counted.
@ -101,18 +114,19 @@ Output info
"""""""""""
This compute calculates a global vector of counts. If the mode is
{atom} or {bond} or {angle} or {dihedral} or {improper}, then the
*atom* or *bond* or *angle* or *dihedral* or *improper*, then the
vector length is the number of atom types or bond types or angle types
or dihedral types or improper types, respectively.
If the mode is {bond} this compute also calculates a global scalar
If the mode is *bond* this compute also calculates a global scalar
which is the number of broken bonds with type = 0, as explained above.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are "extensive".
The scalar and vector values calculated by this compute are both
"intensive".
Restrictions
""""""""""""

2
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@ -106,6 +106,8 @@ Restrictions
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

8
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View File

@ -64,7 +64,7 @@ tangential force tensor. The contact tensor is calculated as
.. math::
C_{ab} = \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab})
C_{ab} = \frac{15}{2} (\phi_{ab} - \frac{1}{3} \mathrm{Tr}(\phi) \delta_{ab})
where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z`
directions, :math:`\delta_{ab}` is the Kronecker delta function, and
@ -83,7 +83,7 @@ The branch tensor is calculated as
.. math::
B_{ab} = \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab})
B_{ab} = \frac{15}{2\, \mathrm{Tr}(D)} (D_{ab} - \frac{1}{3} \mathrm{Tr}(D) \delta_{ab})
where the tensor :math:`D` is defined as
@ -101,7 +101,7 @@ The normal force fabric tensor is calculated as
.. math::
F^n_{ab} = \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab})
F^n_{ab} = \frac{15}{2\, \mathrm{Tr}(N)} (N_{ab} - \frac{1}{3} \mathrm{Tr}(N) \delta_{ab})
where the tensor :math:`N` is defined as
@ -119,7 +119,7 @@ as
.. math::
F^t_{ab} = \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab})
F^t_{ab} = \frac{5}{\mathrm{Tr}(N)} (T_{ab} - \frac{1}{3} \mathrm{Tr}(T) \delta_{ab})
where the tensor :math:`T` is defined as

54
doc/src/compute_mliap.rst
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@ -20,7 +20,7 @@ Syntax
*model* values = style
style = *linear* or *quadratic* or *mliappy*
*descriptor* values = style filename
style = *sna*
style = *sna* or *ace*
filename = name of file containing descriptor definitions
*gradgradflag* value = 0/1
toggle gradgrad method for force gradient
@ -31,6 +31,7 @@ Examples
.. code-block:: LAMMPS
compute mliap model linear descriptor sna Ta06A.mliap.descriptor
compute mliap model linear descriptor ace H_N_O_ccs.yace gradgradflag 1
Description
"""""""""""
@ -40,18 +41,15 @@ of machine-learning interatomic potentials with respect to model parameters.
It is used primarily for calculating the gradient of energy, force, and
stress components with respect to model parameters, which is useful when
training :doc:`mliap pair_style <pair_mliap>` models to match target data.
It provides separate
definitions of the interatomic potential functional form (*model*)
and the geometric quantities that characterize the atomic positions
(*descriptor*). By defining *model* and *descriptor* separately,
It provides separate definitions of the interatomic potential functional
form (*model*) and the geometric quantities that characterize the atomic
positions (*descriptor*). By defining *model* and *descriptor* separately,
it is possible to use many different models with a given descriptor,
or many different descriptors with a given model. Currently, the
compute supports just two models, *linear* and *quadratic*,
and one descriptor, *sna*, the SNAP descriptor used by
:doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
and chem variants. Work is currently underway to extend
the interface to handle neural network energy models,
and it is also straightforward to add new descriptor styles.
or many different descriptors with a given model. Currently, the compute
supports *linear* and *quadratic* SNAP descriptor computes used in
:doc:`pair_style snap <pair_snap>`, *linear* SO3 descriptor computes, and
*linear* ACE descriptor computes used in :doc:`pair_style pace <pair_pace>`,
and it is straightforward to add new descriptor styles.
The compute *mliap* command must be followed by two keywords
*model* and *descriptor* in either order.
@ -60,19 +58,31 @@ The *model* keyword is followed by the model style (*linear*,
*quadratic* or *mliappy*). The *mliappy* model is only available if
LAMMPS is built with the *mliappy* Python module. There are
:ref:`specific installation instructions <mliap>` for that module.
For the *mliap* compute, specifying a *linear* model will compute the
specified descriptors and gradients with respect to linear model parameters
whereas *quadratic* will do the same, but for the quadratic products of
descriptors.
The *descriptor* keyword is followed by a descriptor style, and
additional arguments. The compute currently supports two descriptor
styles *sna* and *so3*, but it is is straightforward to add additional
descriptor styles. The SNAP descriptor style *sna* is the same as that
used by :doc:`pair_style snap <pair_snap>`, including the linear,
quadratic, and chem variants. A single additional argument specifies
the descriptor filename containing the parameters and setting used by
the SNAP descriptor. The descriptor filename usually ends in the
additional arguments. The compute currently supports three descriptor
styles: *sna*, *so3*, and *ace*, but it is is straightforward to add
additional descriptor styles. The SNAP descriptor style *sna* is the
same as that used by :doc:`pair_style snap <pair_snap>`, including the
linear, quadratic, and chem variants. A single additional argument
specifies the descriptor filename containing the parameters and setting used
by the SNAP descriptor. The descriptor filename usually ends in the
*.mliap.descriptor* extension. The format of this file is identical to
the descriptor file in the :doc:`pair_style mliap <pair_mliap>`, and is
described in detail there.
The ACE descriptor style *ace* is the same as :doc:`pair_style pace <pair_pace>`.
A single additional argument specifies the *ace* descriptor filename
that contains parameters and settings for the ACE descriptors. This file
format differs from the SNAP or SO3 descriptor files, and has a *.yace* or
*.ace* extension. However, as with other mliap descriptor styles, this file
is identical to the ace descriptor file in :doc:`pair_style mliap <pair_mliap>`,
where it is described in further detail.
.. note::
The number of LAMMPS atom types (and the value of *nelems* in the model)
@ -172,8 +182,10 @@ This compute is part of the ML-IAP package. It is only enabled if
LAMMPS was built with that package. In addition, building LAMMPS with
the ML-IAP package requires building LAMMPS with the ML-SNAP package.
The *mliappy* model also requires building LAMMPS with the PYTHON
package. See the :doc:`Build package <Build_package>` page for more
info.
package. The *ace* descriptor also requires building LAMMPS with the
ML-PACE package. See the :doc:`Build package <Build_package>` page for
more info. Note that `kk` (KOKKOS) accelerated variants of SNAP and
ACE descriptors are not compatible with `mliap descriptor`.
Related commands
""""""""""""""""

2
doc/src/compute_pace.rst
View File

@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
This compute calculates a set of quantities related to the atomic
cluster expansion (ACE) descriptors of the atoms in a group. ACE

3
doc/src/compute_pressure.rst
View File

@ -153,7 +153,8 @@ Related commands
Default
"""""""
none
By default the compute includes contributions from the keywords:
``ke pair bond angle dihedral improper kspace fix``
----------

3
doc/src/compute_property_atom.rst
View File

@ -23,6 +23,7 @@ Syntax
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
temperature, heatflow,
angmomx, angmomy, angmomz,
shapex, shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
@ -56,6 +57,8 @@ Syntax
*nbonds* = number of bonds assigned to an atom
*radius,diameter* = radius,diameter of spherical particle
*omegax,omegay,omegaz* = angular velocity of spherical particle
*temperature* = internal temperature of spherical particle
*heatflow* = internal heat flow of spherical particle
*angmomx,angmomy,angmomz* = angular momentum of aspherical particle
*shapex,shapey,shapez* = 3 diameters of aspherical particle
*quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

2
doc/src/compute_rattlers_atom.rst
View File

@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a compute that identifies rattlers in a system. Rattlers are often
identified in granular or glassy packings as under-coordinated atoms that

59
doc/src/compute_rdf.rst
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@ -13,8 +13,8 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* rdf = style name of this compute command
* Nbin = number of RDF bins
* itypeN = central atom type for Nth RDF histogram (see asterisk form below)
* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
* itypeN = central atom type for Nth RDF histogram (integer, type label, or asterisk form)
* jtypeN = distribution atom type for Nth RDF histogram (integer, type label, or asterisk form)
* zero or more keyword/value pairs may be appended
* keyword = *cutoff*
@ -96,14 +96,16 @@ is computed for :math:`g(r)` between all atom types. If one or more pairs are
listed, then a separate histogram is generated for each
*itype*,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the fourth example
above. Or a wild-card asterisk can be used to specify a range of atom
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If
:math:`N` is the number of atom types, then an asterisk with no numeric values
means all types from 1 to :math:`N`. A leading asterisk means all types from 1
to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive).
The *itypeN* and *jtypeN* settings can be specified in one of three
ways. One or both of the types in the I,J pair can be a
:doc:`type label <Howto_type_labels>`. Or an explicit numeric value can be
used, as in the fourth example above. Or a wild-card asterisk can be used
to specify a range of atom types. This takes the form "\*" or "\*n" or
"m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk
with no numeric values means all types from 1 to :math:`N`. A leading
asterisk means all types from 1 to n (inclusive). A trailing asterisk
means all types from m to :math:`N` (inclusive). A middle asterisk means
all types from m to n (inclusive).
If both *itypeN* and *jtypeN* are single values, as in the fourth example
above, this means that a :math:`g(r)` is computed where atoms of type *itypeN*
@ -176,22 +178,29 @@ also numbers :math:`\ge 0.0`.
Restrictions
""""""""""""
The RDF is not computed for distances longer than the force cutoff,
since processors (in parallel) do not know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger
distances, you can use the :doc:`rerun <rerun>` command to post-process
a dump file and set the cutoff for the potential to be longer in the
By default, the RDF is not computed for distances longer than the
largest force cutoff, since the neighbor list creation will only contain
pairs up to that distance (plus neighbor list skin). This distance can
be increased using the *cutoff* keyword but this keyword is only valid
with :doc:`neighbor styles 'bin' and 'nsq' <neighbor>`.
If you want an RDF for larger distances, you can also use the
:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
style zero <pair_zero>` and set the force cutoff to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you are not running dynamics and thus are not changing
your model. The definition of :math:`g(r)` used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)`
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else.
The function :math:`\text{coord}(r)` will show a step
change from zero to one at the location of the spike in :math:`g(r)`.
arbitrary and with pair style zero you are not computing any forces, and
you are not running dynamics you are not changing the model that
generated the trajectory.
The definition of :math:`g(r)` used by LAMMPS is only appropriate for
characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still correct
and meaningful. As an example, if a large simulation cell contains only
one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` will
register an arbitrarily large spike at whatever distance they happen to
be at, and zero everywhere else. The function :math:`\text{coord}(r)`
will show a step change from zero to one at the location of the spike in
:math:`g(r)`.
.. note::

2
doc/src/compute_reaxff_atom.rst
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@ -40,7 +40,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a computation that extracts bond information computed by the ReaxFF
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.

3
doc/src/compute_reduce.rst
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@ -56,8 +56,9 @@ Examples
compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE inputs peratom
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
compute 4 all reduce max c_bond inputs local
Description
"""""""""""

2
doc/src/compute_slcsa_atom.rst
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@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a computation that performs the Supervised Learning Crystal
Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`

3
doc/src/compute_stress_atom.rst
View File

@ -289,7 +289,8 @@ Related commands
Default
"""""""
none
By default the compute includes contributions from the keywords:
``ke pair bond angle dihedral improper kspace fix``
----------

9
doc/src/compute_stress_mop.rst
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@ -126,16 +126,19 @@ These styles are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS is built with that package. See the :doc:`Build
package <Build_package>` doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
The method is implemented for orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
interactions, long range (kspace) interactions and
*stress/mop/profile* and *stress/mop* do not work with more than two-body
pair interactions, long range (kspace) interactions and
improper intramolecular interactions.
The impact of fixes that affect the stress (e.g. fix langevin) is
also not included in the stress computed here.
Related commands
""""""""""""""""

277
doc/src/create_atoms.rst
View File

@ -10,7 +10,7 @@ Syntax
create_atoms type style args keyword values ...
* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
* type = atom type (1-Ntypes or type label) of atoms to create (offset for molecule creation)
* style = *box* or *region* or *single* or *mesh* or *random*
.. parsed-literal::
@ -37,7 +37,7 @@ Syntax
seed = random # seed (positive integer)
*basis* values = M itype
M = which basis atom
itype = atom type (1-N) to assign to this basis atom
itype = atom type (1-Ntypes or type label) to assign to this basis atom
*ratio* values = frac seed
frac = fraction of lattice sites (0 to 1) to populate randomly
seed = random # seed (positive integer)
@ -74,6 +74,13 @@ Examples
.. code-block:: LAMMPS
create_atoms 1 box
labelmap atom 1 Pt
create_atoms Pt box
labelmap atom 1 C 2 Si
create_atoms C region regsphere basis Si C
create_atoms 3 region regsphere basis 2 3
create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
create_atoms 3 single 0 0 5
@ -86,25 +93,46 @@ Description
"""""""""""
This command creates atoms (or molecules) within the simulation box,
either on a lattice, or a single atom (or molecule), or on a surface
defined by a triangulated mesh, or a random collection of atoms (or
molecules). It is an alternative to reading in atom coordinates
either on a lattice, or at random points, or on a surface defined by a
triangulated mesh. Or it creates a single atom (or molecule) at a
specified point. It is an alternative to reading in atom coordinates
explicitly via a :doc:`read_data <read_data>` or :doc:`read_restart
<read_restart>` command. A simulation box must already exist, which is
<read_restart>` command.
To use this command a simulation box must already exist, which is
typically created via the :doc:`create_box <create_box>` command.
Before using this command, a lattice must also be defined using the
:doc:`lattice <lattice>` command, unless you specify the *single* style
with units = box or the *random* style. For the remainder of this doc
page, a created atom or molecule is referred to as a "particle".
Before using this command, a lattice must typically also be defined
using the :doc:`lattice <lattice>` command, unless you specify the
*single* or *mesh* style with units = box or the *random* style. To
create atoms on a lattice for general triclinic boxes, see the
discussion below.
For the remainder of this doc page, a created atom or molecule is
referred to as a "particle".
If created particles are individual atoms, they are assigned the
specified atom *type*, though this can be altered via the *basis*
keyword as discussed below. If molecules are being created, the type
of each atom in the created molecule is specified in the file read by
the :doc:`molecule <molecule>` command, and those values are added to
the specified atom *type* (e.g., if *type* = 2 and the file specifies
atom types 1, 2, and 3, then each created molecule will have atom types
3, 4, and 5).
of each atom in the created molecule is specified in a specified file
read by the :doc:`molecule <molecule>` command, and those values are
added to the specified atom *type* (e.g., if *type* = 2 and the file
specifies atom types 1, 2, and 3, then each created molecule will have
atom types 3, 4, and 5).
.. note::
You cannot use this command to create atoms that are outside the
simulation box; they will just be ignored by LAMMPS. This is true
even if you are using shrink-wrapped box boundaries, as specified
by the :doc:`boundary <boundary>` command. However, you can first
use the :doc:`change_box <change_box>` command to temporarily
expand the box, then add atoms via create_atoms, then finally use
change_box command again if needed to re-shrink-wrap the new atoms.
See the :doc:`change_box <change_box>` doc page for an example of
how to do this, using the create_atoms *single* style to insert a
new atom outside the current simulation box.
----------
For the *box* style, the create_atoms command fills the entire
simulation box with particles on the lattice. If your simulation box
@ -126,10 +154,117 @@ periodic boundaries. If this is desired, you should either use the
*box* style, or tweak the region size to get precisely the particles
you want.
----------
If the simulation box is formulated as a general triclinic box defined
by arbitrary edge vectors **A**, **B**, **C**, then the *box* and
*region* styles will create atoms on a lattice commensurate with those
edge vectors. See the :doc:`Howto_triclinic <Howto_triclinic>` doc
page for a detailed explanation of orthogonal, restricted triclinic,
and general triclinic simulation boxes. As with the :doc:`create_box
<create_box>` command, the :doc:`lattice <lattice>` command used by
this command must be of style *custom* and use its *triclinic/general*
option. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
command define the edge vectors of a unit cell of the general
triclinic lattice. The :doc:`create_box <create_box>` command creates
a simulation box which replicates that unit cell along each of the
**A**, **B**, **C** edge vectors.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box created by the :doc:`create_box <create_box>` command as
well as the atoms created by this command with their per-atom
information (e.g. coordinates, velocities) are converted (rotated)
from general to restricted triclinic form when the two commands are
invoked. The <Howto_triclinic>` doc page also discusses other
LAMMPS commands which can input/output general triclinic
representations of the simulation box and per-atom data.
The *box* style will fill the entire general triclinic box with
particles on the lattice, as explained above.
.. note::
The *region* style also operates as explained above, but the check
for particles inside the region is performed *after* the particle
coordinates have been converted to the restricted triclinic box.
This means the region must also be defined with respect to the
restricted triclinic box, not the general triclinic box.
If the simulation box is general triclinic, the *single*, *random*,
and *mesh* styles described next operate on the box *after* it has
been converted to restricted triclinic. So all the settings for those
styles should be made in that context.
----------
For the *single* style, a single particle is added to the system at
the specified coordinates. This can be useful for debugging purposes
or to create a tiny system with a handful of particles at specified
positions.
positions. For a 2d simulation the specified z coordinate must be
0.0.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. For 2d simulations, the z coordinates of all added
atoms will be 0.0.
The particles are created one by one using the specified random number
*seed*, resulting in the same set of particle coordinates, independent
of how many processors are being used in the simulation. Unless the
*overlap* keyword is specified, particles created by the *random*
style will typically be highly overlapped. Various additional
criteria can be used to accept or reject a random particle insertion;
see the keyword discussion below. Multiple attempts per particle are
made (see the *maxtry* keyword) until the insertion is either
successful or fails. If this command fails to add all requested *N*
particles, a warning will be output.
If the *region-ID* argument is specified as NULL, then the randomly
created particles will be anywhere in the simulation box. If a
*region-ID* is specified, a geometric volume is filled that is both
inside the simulation box and is also consistent with the region
volume. See the :doc:`region <region>` command for details. Note
that a region can be specified so that its "volume" is either inside
or outside its geometric boundary.
Note that the create_atoms command adds particles to those that
already exist. This means it can be used to add particles to a system
previously read in from a data or restart file. Or the create_atoms
command can be used multiple times, to add multiple sets of particles
to the simulation. For example, grain boundaries can be created, by
interleaving the create_atoms command with :doc:`lattice <lattice>`
commands specifying different orientations.
When this command is used, care should be taken to ensure the
resulting system does not contain particles that are highly
overlapped. Such overlaps will cause many interatomic potentials to
compute huge energies and forces, leading to bad dynamics. There are
several strategies to avoid this problem:
* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
create_atoms. For example, this strategy can be used to overlay and
surround a large protein molecule with a volume of water molecules,
then delete water molecules that overlap with the protein atoms.
* For the *random* style, use the optional *overlap* keyword to avoid
overlaps when each new particle is created.
* Before running dynamics on an overlapped system, perform an
:doc:`energy minimization <minimize>`. Or run initial dynamics with
:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
<fix_nve_limit>` to un-overlap the particles, before running normal
dynamics.
.. figure:: img/marble_race.jpg
:figwidth: 33%
@ -189,73 +324,6 @@ to the area of that triangle.
beneficial to exclude computing interactions between the created
particles using :doc:`neigh_modify exclude <neigh_modify>`.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
specified random number *seed*, resulting in the same set of particle
coordinates, independent of how many processors are being used in the
simulation. Unless the *overlap* keyword is specified, particles
created by the *random* style will typically be highly overlapped.
Various additional criteria can be used to accept or reject a random
particle insertion; see the keyword discussion below. Multiple
attempts per particle are made (see the *maxtry* keyword) until the
insertion is either successful or fails. If this command fails to add
all requested *N* particles, a warning will be output.
If the *region-ID* argument is specified as NULL, then the randomly
created particles will be anywhere in the simulation box. If a
*region-ID* is specified, a geometric volume is filled that is both
inside the simulation box and is also consistent with the region
volume. See the :doc:`region <region>` command for details. Note
that a region can be specified so that its "volume" is either inside
or outside its geometric boundary.
Note that the create_atoms command adds particles to those that
already exist. This means it can be used to add particles to a system
previously read in from a data or restart file. Or the create_atoms
command can be used multiple times, to add multiple sets of particles
to the simulation. For example, grain boundaries can be created, by
interleaving the create_atoms command with :doc:`lattice <lattice>`
commands specifying different orientations.
When this command is used, care should be taken to ensure the
resulting system does not contain particles that are highly
overlapped. Such overlaps will cause many interatomic potentials to
compute huge energies and forces, leading to bad dynamics. There are
several strategies to avoid this problem:
* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
create_atoms. For example, this strategy can be used to overlay and
surround a large protein molecule with a volume of water molecules,
then delete water molecules that overlap with the protein atoms.
* For the *random* style, use the optional *overlap* keyword to avoid
overlaps when each new particle is created.
* Before running dynamics on an overlapped system, perform an
:doc:`energy minimization <minimize>`. Or run initial dynamics with
:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
<fix_nve_limit>` to un-overlap the particles, before running normal
dynamics.
.. note::
You cannot use any of the styles explained above to create atoms
that are outside the simulation box; they will just be ignored by
LAMMPS. This is true even if you are using shrink-wrapped box
boundaries, as specified by the :doc:`boundary <boundary>` command.
However, you can first use the :doc:`change_box <change_box>`
command to temporarily expand the box, then add atoms via
create_atoms, then finally use change_box command again if needed
to re-shrink-wrap the new atoms. See the :doc:`change_box
<change_box>` doc page for an example of how to do this, using the
create_atoms *single* style to insert a new atom outside the
current simulation box.
----------
Individual atoms are inserted by this command, unless the *mol*
@ -268,6 +336,12 @@ molecule can be specified in the molecule file. See the
required to be in this file are the coordinates and types of atoms in
the molecule.
.. note::
If you are using the *mol* keyword in combination with the
:doc:`atom style template <atom_style>` command, they must use
the same molecule template-ID.
Using a lattice to add molecules, e.g. via the *box* or *region* or
*single* styles, is exactly the same as adding atoms on lattice
points, except that entire molecules are added at each point, i.e. on
@ -401,12 +475,13 @@ to.
The *overlap* keyword only applies to the *random* style. It prevents
newly created particles from being created closer than the specified
*Doverlap* distance from any other particle. When the particles being
created are molecules, the radius of the molecule (from its geometric
center) is added to *Doverlap*. If particles have finite size (see
:doc:`atom_style sphere <atom_style>` for example) *Doverlap* should
be specified large enough to include the particle size in the
non-overlapping criterion.
*Doverlap* distance from any other particle. If particles have finite
size (see :doc:`atom_style sphere <atom_style>` for example) *Doverlap*
should be specified large enough to include the particle size in the
non-overlapping criterion. If molecules are being randomly inserted, then
an insertion is only accepted if each particle in the molecule meets the
overlap criterion with respect to other particles (not including particles
in the molecule itself).
.. note::
@ -463,12 +538,19 @@ on a single CPU core.
-----
The *units* keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the *single*
style, or the overlap distance *Doverlap* by the *overlap* keyword. A
*box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\AA` for
units = *real* or *metal*\ . A *lattice* value means the distance units are in
lattice spacings.
by parameters for various styles. A *box* value selects standard
distance units as defined by the :doc:`units <units>` command (e.g.,
:math:`\AA` for units = *real* or *metal*\ . A *lattice* value means
the distance units are in lattice spacings. These are affected settings:
* for *single* style: coordinates of the particle created
* for *random* style: overlap distance *Doverlap* by the *overlap* keyword
* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect*
* for *mesh* style: *radthresh* value for *meshmode* = *bisect*
* for *mesh* style: *density* value for *meshmode* = *qrand*
Since *density* represents an area (distance ^2), the lattice spacing
factor is also squared.
----------
@ -536,6 +618,11 @@ command.
A rotation vector specified for a single molecule must be in
the z-direction for a 2d model.
For :doc:`molecule templates <molecule>` that are created from multiple
files, i.e. contain multiple molecule *sets*, only the first set is
used. To create multiple molecules the files currently need to be
merged and different molecule IDs assigned with a Molecules section.
Related commands
""""""""""""""""

241
doc/src/create_box.rst
View File

@ -9,9 +9,11 @@ Syntax
.. code-block:: LAMMPS
create_box N region-ID keyword value ...
create_box N NULL alo ahi blo bhi clo chi keyword value ...
* N = # of atom types to use in this simulation
* region-ID = ID of region to use as simulation domain
* region-ID = ID of region to use as simulation domain or NULL for general triclinic box
* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice <lattice>` command (only when region-ID = NULL)
* zero or more keyword/value pairs may be appended
* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
@ -32,121 +34,204 @@ Examples
.. code-block:: LAMMPS
# orthogonal or restricted triclinic box using regionID = mybox
create_box 2 mybox
create_box 2 mybox bond/types 2 extra/bond/per/atom 1
.. code-block:: LAMMPS
# 2d general triclinic box using primitive cell for 2d hex lattice
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
create_box 1 NULL 0 5 0 5 -0.5 0.5
.. code-block:: LAMMPS
# 3d general triclinic box using primitive cell for 3d fcc lattice
lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
create box 1 NULL -5 5 -10 10 0 20
Description
"""""""""""
This command creates a simulation box based on the specified region.
Thus a :doc:`region <region>` command must first be used to define a
geometric domain. It also partitions the simulation box into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors being used and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
This command creates a simulation box. It also partitions the box into
a regular 3d grid of smaller sub-boxes, one per processor (MPI task).
The geometry of the partitioning is based on the size and shape of the
simulation box, the number of processors being used and the settings
of the :doc:`processors <processors>` command. The partitioning can
later be changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
The argument N is the number of atom types that will be used in the
Simulation boxes in LAMMPS can be either orthogonal or triclinic in
shape. Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6
faces that are each perpendicular to one of the standard xyz
coordinate axes. Triclinic boxes are a parallelepiped in 3d
(parallelogram in 2d) with opposite pairs of faces parallel to each
other. LAMMPS supports two forms of triclinic boxes, restricted and
general, which differ in how the box is oriented with respect to the
xyz coordinate axes. See the :doc:`Howto triclinic <Howto_triclinic>`
for a detailed description of all 3 kinds of simulation boxes.
The argument *N* is the number of atom types that will be used in the
simulation.
Orthogonal and restricted triclinic boxes are created by specifying a
region ID previously defined by the :doc:`region <region>` command.
General triclinic boxes are discussed below.
If the region is not of style *prism*, then LAMMPS encloses the region
(block, sphere, etc.) with an axis-aligned orthogonal bounding box
which becomes the simulation domain.
which becomes the simulation domain. For a 2d simulation, the zlo and
zhi values of the simulation box must straddle zero.
If the region is of style *prism*, LAMMPS creates a non-orthogonal
simulation domain shaped as a parallelepiped with triclinic symmetry.
As defined by the :doc:`region prism <region>` command, the
parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by three
edge vectors starting from the origin given by
:math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`;
:math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and
:math:`\vec c = (xz,yz,z_\text{hi}-z_\text{lo})`.
The parameters *xy*\ , *xz*\ , and *yz* can be 0.0 or
positive or negative values and are called "tilt factors" because they
are the amount of displacement applied to faces of an originally
orthogonal box to transform it into the parallelepiped.
parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors
starting from the origin given by :math:`\vec a =
(x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b =
(xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c =
(xz,yz,z_\text{hi}-z_\text{lo})`. In LAMMPS lingo, this is a
restricted triclinic box because the three edge vectors cannot be
defined in arbitrary (general) directions. The parameters *xy*\ ,
*xz*\ , and *yz* can be 0.0 or positive or negative values and are
called "tilt factors" because they are the amount of displacement
applied to faces of an originally orthogonal box to transform it into
the parallelepiped. For a 2d simulation, the zlo and zhi values of
the simulation box must straddle zero.
By default, a *prism* region used with the create_box command must have
tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
the distance of the parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
Typically a *prism* region used with the create_box command should
have tilt factors :math:`(xy,xz,yz)` that do not skew the box more
than half the distance of the parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the
:math:`x` box length is 10 and the :math:`xy` tilt factor must be
between :math:`-5` and :math:`5`. Similarly, both :math:`xz` and
:math:`yz` must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt :math:`= \dots, -15`,
:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` are all
geometrically equivalent.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
LAMMPS will issue a warning if the tilt factors of the created box do
not meet this criterion. This is because simulations with large tilt
factors may run inefficiently, since they require more ghost atoms and
thus more communication. With very large tilt factors, LAMMPS may
eventually produce incorrect trajectories and stop with errors due to
lost atoms or similar issues.
When a prism region is used, the simulation domain should normally be periodic
in the dimension that the tilt is applied to, which is given by the second
dimension of the tilt factor (e.g., :math:`y` for :math:`xy` tilt). This is so
that pairs of atoms interacting across that boundary will have one of them
shifted by the tilt factor. Periodicity is set by the
:doc:`boundary <boundary>` command. For example, if the :math:`xy` tilt factor
is non-zero, then the :math:`y` dimension should be periodic. Similarly, the
:math:`z` dimension should be periodic if :math:`xz` or :math:`yz` is non-zero.
LAMMPS does not require this periodicity, but you may lose atoms if this is not
the case.
See the :doc:`Howto triclinic <Howto_triclinic>` page for geometric
descriptions of triclinic boxes and tilt factors, as well as how to
transform the restricted triclinic parameters to and from other
commonly used triclinic representations.
When a prism region is used, the simulation domain should normally be
periodic in the dimension that the tilt is applied to, which is given
by the second dimension of the tilt factor (e.g., :math:`y` for
:math:`xy` tilt). This is so that pairs of atoms interacting across
that boundary will have one of them shifted by the tilt factor.
Periodicity is set by the :doc:`boundary <boundary>` command. For
example, if the :math:`xy` tilt factor is non-zero, then the :math:`y`
dimension should be periodic. Similarly, the :math:`z` dimension
should be periodic if :math:`xz` or :math:`yz` is non-zero. LAMMPS
does not require this periodicity, but you may lose atoms if this is
not the case.
Note that if your simulation will tilt the box (e.g., via the
:doc:`fix deform <fix_deform>` command), the simulation box must be set up to
be triclinic, even if the tilt factors are initially 0.0. You can
also change an orthogonal box to a triclinic box or vice versa by
:doc:`fix deform <fix_deform>` command), the simulation box must be
created as triclinic, even if the tilt factors are initially 0.0. You
can also change an orthogonal box to a triclinic box or vice versa by
using the :doc:`change box <change_box>` command with its *ortho* and
*triclinic* options.
.. note::
If the system is non-periodic (in a dimension), then you should
not make the lo/hi box dimensions (as defined in your
:doc:`region <region>` command) radically smaller/larger than the extent
of the atoms you eventually plan to create (e.g., via the
:doc:`create_atoms <create_atoms>` command). For example, if your atoms
extend from 0 to 50, you should not specify the box bounds as :math:`-10000`
and :math:`10000`. This is because as described above, LAMMPS uses the
specified box size to lay out the 3d grid of processors. A huge
(mostly empty) box will be sub-optimal for performance when using
"fixed" boundary conditions (see the :doc:`boundary <boundary>`
command). When using "shrink-wrap" boundary conditions (see the
:doc:`boundary <boundary>` command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms.
If the system is non-periodic (in a dimension), then you should not
make the lo/hi box dimensions (as defined in your :doc:`region
<region>` command) radically smaller/larger than the extent of the
atoms you eventually plan to create (e.g., via the
:doc:`create_atoms <create_atoms>` command). For example, if your
atoms extend from 0 to 50, you should not specify the box bounds as
:math:`-10000` and :math:`10000`. This is because as described
above, LAMMPS uses the specified box size to lay out the 3d grid of
processors. A huge (mostly empty) box will be sub-optimal for
performance when using "fixed" boundary conditions (see the
:doc:`boundary <boundary>` command). When using "shrink-wrap"
boundary conditions (see the :doc:`boundary <boundary>` command), a
huge (mostly empty) box may cause a parallel simulation to lose
atoms the first time that LAMMPS shrink-wraps the box around the
atoms.
----------
As noted above, general triclinic boxes in LAMMPS allow the box to
have arbitrary edge vectors **A**, **B**, **C**. The only
restrictions are that the three vectors be distinct, non-zero, and not
co-planar. They must also define a right-handed system such that
(**A** x **B**) points in the direction of **C**. Note that a
left-handed system can be converted to a right-handed system by simply
swapping the order of any pair of the **A**, **B**, **C** vectors.
To create a general triclinic boxes, the region is specified as NULL
and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three
edge vectors **A**, **B**, **C** using additional information
previously defined by the :doc:`lattice <lattice>` command.
The lattice must be of style *custom* and use its *triclinic/general*
option. This insures the lattice satisfies the restrictions listed
above. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
command define the edge vectors of a unit cell of the general
triclinic lattice. This command uses them to define the three edge
vectors and origin of the general triclinic box as:
* **A** = (ahi-alo) * *a1*
* **B** = (bhi-blo) * *a2*
* **C** = (chi-clo) * *a3*
* origin = (alo*a1 + blo*a2 + clo*a3)
For 2d general triclinic boxes, clo = -0.5 and chi = 0.5 is required.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box defined by this command and per-atom information
(e.g. coordinates, velocities) defined by the :doc:`create_atoms
<create_atoms>` command are converted (rotated) from general to
restricted triclinic form when the two commands are invoked. The
<Howto_triclinic>` doc page also discusses other LAMMPS commands
which can input/output general triclinic representations of the
simulation box and per-atom data.
----------
The optional keywords can be used to create a system that allows for
bond (angle, dihedral, improper) interactions, or for molecules with
special 1--2, 1--3, or 1--4 neighbors to be added later. These optional
keywords serve the same purpose as the analogous keywords that can be
used in a data file which are recognized by the
special 1--2, 1--3, or 1--4 neighbors to be added later. These
optional keywords serve the same purpose as the analogous keywords
that can be used in a data file which are recognized by the
:doc:`read_data <read_data>` command when it sets up a system.
Note that if these keywords are not used, then the create_box command
creates an atomic (non-molecular) simulation that does not allow bonds
between pairs of atoms to be defined, or a
:doc:`bond potential <bond_style>` to be specified, or for molecules with
special neighbors to be added to the system by commands such as
:doc:`create_atoms mol <create_atoms>`, :doc:`fix deposit <fix_deposit>`
or :doc:`fix pour <fix_pour>`.
between pairs of atoms to be defined, or a :doc:`bond potential
<bond_style>` to be specified, or for molecules with special neighbors
to be added to the system by commands such as :doc:`create_atoms mol
<create_atoms>`, :doc:`fix deposit <fix_deposit>` or :doc:`fix pour
<fix_pour>`.
As an example, see the examples/deposit/in.deposit.molecule script,
which deposits molecules onto a substrate. Initially there are no
molecules in the system, but they are added later by the
:doc:`fix deposit <fix_deposit>` command. The create_box command in the
script uses the bond/types and extra/bond/per/atom keywords to allow
this. If the added molecule contained more than one special bond
(allowed by default), an extra/special/per/atom keyword would also
need to be specified.
molecules in the system, but they are added later by the :doc:`fix
deposit <fix_deposit>` command. The create_box command in the script
uses the bond/types and extra/bond/per/atom keywords to allow this.
If the added molecule contained more than one special bond (allowed by
default), an extra/special/per/atom keyword would also need to be
specified.
----------

24
doc/src/delete_bonds.rst
View File

@ -43,6 +43,9 @@ Examples
delete_bonds all bond 0*3 special
delete_bonds all stats
labelmap atom 4 hc
delete_bonds all atom hc special
Description
"""""""""""
@ -59,19 +62,20 @@ For all styles, by default, an interaction is only turned off (or on)
if all the atoms involved are in the specified group. See the *any*
keyword to change the behavior.
Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*,
*improper*\ ) take a *type* as an argument. The specified *type* should
be an integer from 0 to :math:`N`, where :math:`N` is the number of relevant
Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ )
take a *type* as an argument. The specified *type* can be a
:doc:`type label <Howto_type_labels>`. Otherwise, the type should be an
integer from 0 to :math:`N`, where :math:`N` is the number of relevant
types (atom types, bond types, etc.). A value of 0 is only relevant for
style *bond*\ ; see details below. In all cases, a wildcard asterisk
style *bond*\ ; see details below. For numeric types, a wildcard asterisk
can be used in place of or in conjunction with the *type* argument to
specify a range of types. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the number of types, then an asterisk with no numeric
values means all types from 0 to :math:`N`. A leading asterisk means all
types from 0 to n (inclusive). A trailing asterisk means all types
from m to N (inclusive). A middle asterisk means all types from m to
n (inclusive). Note that it is fine to include a type of 0 for
non-bond styles; it will simply be ignored.
"m\*n". If :math:`N` is the number of types, then an asterisk with no
numeric values means all types from 0 to :math:`N`. A leading asterisk
means all types from 0 to n (inclusive). A trailing asterisk means all
types from m to N (inclusive). A middle asterisk means all types from m to
n (inclusive). Note that it is fine to include a type of 0 for non-bond
styles; it will simply be ignored.
For style *multi* all bond, angle, dihedral, and improper interactions
of any type, involving atoms in the group, are turned off.

7
doc/src/dihedral_charmm.rst
View File

@ -3,6 +3,7 @@
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
.. index:: dihedral_style charmmfsw/kk
dihedral_style charmm command
=============================
@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
dihedral_style charmmfsw command
================================
Accelerator Variants: *charmmfsw/kk*
Syntax
""""""
@ -144,7 +147,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

71
doc/src/dihedral_cosine_squared_restricted.rst Normal file
View File

@ -0,0 +1,71 @@
.. index:: dihedral_style cosine/squared/restricted
dihedral_style cosine/squared/restricted command
================================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style cosine/squared/restricted
Examples
""""""""
.. code-block:: LAMMPS
dihedral_style cosine/squared/restricted
dihedral_coeff 1 10.0 120
Description
"""""""""""
.. versionadded:: 17Apr2024
The *cosine/squared/restricted* dihedral style uses the potential
.. math::
E = K [\cos(\phi) - \cos(\phi_0)]^2 / \sin^2(\phi)
, which is commonly used in the MARTINI force field.
See :ref:`(Bulacu) <restricted-Bul>` for a description of the restricted dihedral for the MARTINI force field.
The following coefficients must be defined for each dihedral type via the
:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`\phi_0` (degrees)
:math:`\phi_0` is specified in degrees, but LAMMPS converts it to radians internally.
----------
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
Default
"""""""
none
----------
.. _restricted-Bul:
**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
(2013).

3
doc/src/dihedral_style.rst
View File

@ -10,7 +10,7 @@ Syntax
dihedral_style style
* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *cosine/squared/restricted* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
Examples
""""""""
@ -105,6 +105,7 @@ exist.
* :doc:`charmmfsw <dihedral_charmm>` - CHARMM dihedral with force switching
* :doc:`class2 <dihedral_class2>` - COMPASS (class 2) dihedral
* :doc:`cosine/shift/exp <dihedral_cosine_shift_exp>` - dihedral with exponential in spring constant
* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` - squared cosine dihedral with restricted term
* :doc:`fourier <dihedral_fourier>` - dihedral with multiple cosine terms
* :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral
* :doc:`helix <dihedral_helix>` - helix dihedral

139
doc/src/dump.rst
View File

@ -104,7 +104,6 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
heatflow, temperature,
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
i_name, d_name, i2_name[I], d2_name[I]
@ -115,6 +114,7 @@ Syntax
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
typelabel = atom :doc:`type label <Howto_type_labels>`
element = name of atom element, as defined by :doc:`dump_modify <dump_modify>` command
mass = atom mass
x,y,z = unscaled atom coordinates
@ -131,8 +131,6 @@ Syntax
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
heatflow = rate of heat flow into particle
temperature = temperature of particle
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID
@ -278,16 +276,20 @@ format <dump_modify>` command and its options.
Format of native LAMMPS format dump files:
The *atom*, *custom*, *grid*, and *local* styles create files in a
simple LAMMPS-specific text format that is self-explanatory when
viewing a dump file. Many post-processing tools either included with
LAMMPS or third-party tools can read this format, as does the
simple LAMMPS-specific text format that is mostly self-explanatory
when viewing a dump file. Many post-processing tools either included
with LAMMPS or third-party tools can read this format, as does the
:doc:`rerun <rerun>` command. See tools described on the :doc:`Tools
<Tools>` doc page for examples, including `Pizza.py
<https://lammps.github.io/pizza>`_.
For all these styles, the dimensions of the simulation box are
included in each snapshot. For an orthogonal simulation box this
information is formatted as:
included in each snapshot. The simulation box in LAMMPS can be
defined in one of 3 ways: orthogonal, restricted triclinic, and
general triclinic. See the :doc:`Howto triclinic <Howto_triclinic>`
doc page for a detailed description of all 3 options.
For an orthogonal simulation box the box information is formatted as:
.. parsed-literal::
@ -304,10 +306,10 @@ the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
or *m* (shrink wrapped with a minimum value). See the
:doc:`boundary <boundary>` command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
formatted as follows:
For a restricted triclinic simulation box, an orthogonal bounding box
which encloses the restricted triclinic simulation box is output,
along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic
box, formatted as follows:
.. parsed-literal::
@ -329,6 +331,10 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the
triclinic parameters, and how to transform those parameters to and
from other commonly used triclinic representations.
For a general triclinic simulation box, see the "General triclinic"
section below for a description of the ITEM: BOX BOUNDS format as well
as how per-atom coordinates and per-atom vector quantities are output.
The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line
with the count of atoms in the snapshot. Likewise they output an
"ITEM: ATOMS" line which includes column descriptors for the per-atom
@ -400,7 +406,6 @@ command.
Dump files in other popular formats:
.. note::
This section only discusses file formats relevant to this doc page.
@ -466,8 +471,9 @@ followed by one line per atom with the atom type and the :math:`x`-,
:math:`y`-, and :math:`z`-coordinate of that atom. You can use the
:doc:`dump_modify element <dump_modify>` option to change the output
from using the (numerical) atom type to an element name (or some other
label). This will help many visualization programs to guess bonds and
colors.
label). This option will help many visualization programs to guess bonds
and colors. You can use the :doc:`dump_modify types labels <dump_modify>`
option to replace numeric atom types with :doc:`type labels <Howto_type_labels>`.
.. versionadded:: 22Dec2022
@ -656,6 +662,87 @@ how to control the compression level in both variants.
----------
General triclinic simulation box output for the *atom* and *custom* styles:
As mentioned above, the simulation box can be defined as a general
triclinic box, which means that 3 arbitrary box edge vectors **A**,
**B**, **C** can be specified. See the :doc:`Howto triclinic
<Howto_triclinic>` doc page for a detailed description of general
triclinic boxes.
This option is provided as a convenience for users who may be
converting data from solid-state crystallographic representations or
from DFT codes for input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally, LAMMPS
only uses restricted triclinic simulation boxes. This means the box
and per-atom information (e.g. coordinates, velocities) LAMMPS stores
are converted (rotated) from general to restricted triclinic form when
the system is created.
For dump output, if the :doc:`dump_modify triclinic/general
<dump_modify>` command is used, the box description and per-atom
coordinates and other per-atom vectors will be converted (rotated)
from restricted to general form when each dump file snapshots is
output. This option can only be used if the simulation box was
initially created as general triclinic. If the option is not used,
and the simulation box is general triclinic, then the dump file
snapshots will reflect the internal restricted triclinic geometry.
The dump_modify triclinic/general option affects 3 aspects of the dump
file output.
First, the format for the BOX BOUNDS is as follows
.. parsed-literal::
ITEM: BOX BOUNDS abc origin
ax ay az originx
bx by bz originy
cx cy cz originz
where the **A** edge vector of the box is (ax,ay,az) and similarly
for **B** and **C**. The origin of all 3 edge vectors is (originx,
originy, originz).
Second, the coordinates of each atom are converted (rotated) so that
the atom is inside (or near) the general triclinic box defined by the
**A**, **B**, **C** edge vectors. For style *atom*, this only alters
output for unscaled atom coords, via the :doc:`dump_modify scaled no
<dump_modify>` setting. For style *custom*, this alters output for
either unscaled or unwrapped output of atom coords, via the *x,y,z* or
*xu,yu,zu* attributes. For output of scaled atom coords by both
styles, there is no difference between restricted and general
triclinic values.
Third, the output for any attribute of the *custom* style which
represents a per-atom vector quantity will be converted (rotated) to
be oriented consistent with the general triclinic box and its
orientation relative to the standard xyz coordinate axes.
This applies to the following *custom* style attributes:
* vx,vy,vz = atom velocities
* fx,fy,fz = forces on atoms
* mux,muy,muz = orientation of dipole moment of atom
* omegax,omegay,omegaz = angular velocity of spherical particle
* angmomx,angmomy,angmomz = angular momentum of aspherical particle
* tqx,tqy,tqz = torque on finite-size particles
For example, if the velocity of an atom in a restricted triclinic box
is along the x-axis, then it will be output for a general triclinic
box as a vector along the **A** edge vector of the box.
.. note::
For style *custom*, the :doc:`dump_modify thresh <dump_modify>`
command may access per-atom attributes either directly or
indirectly through a compute or variable. If the attribute is an
atom coordinate or one of the vectors mentioned above, its value
will *NOT* be a general triclinic (rotated) value. Rather it will
be a restricted triclinic value.
----------
Arguments for different styles:
The sections below describe per-atom, local, and per grid cell
@ -689,21 +776,21 @@ command creates a per-atom array with six columns:
Per-atom attributes used as arguments to the *custom* and *cfg* styles:
The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
The *id*, *mol*, *proc*, *procp1*, *type*, *typelabel*, *element*, *mass*,
*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
*Id* is the atom ID. *Mol* is the molecule ID, included in the data
file for molecular systems. *Proc* is the ID of the processor (0 to
*Id* is the atom ID. *Mol* is the molecule ID, included in the data file
for molecular systems. *Proc* is the ID of the processor (0 to
:math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the
proc ID+1, which can be convenient in place of a *type* attribute (1 to
:math:`N_\text{types}`) for coloring atoms in a visualization program.
*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
typically the chemical name of an element, which you must assign to each
type via the :doc:`dump_modify element <dump_modify>` command. More
generally, it can be any string you wish to associated with an atom
type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
*fy*, *fz*, and *q* are components of atom velocity and force and atomic
charge.
*Type* is the atom type (1 to :math:`N_\text{types}`). *Typelabel* is the
atom :doc:`type label <Howto_type_labels>`. *Element* is typically the
chemical name of an element, which you must assign to each type via the
:doc:`dump_modify element <dump_modify>` command. More generally, it can
be any string you wish to associated with an atom type. *Mass* is the atom
mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are
components of atom velocity and force and atomic charge.
There are several options for outputting atom coordinates. The *x*,
*y*, and *z* attributes write atom coordinates "unscaled", in the

57
doc/src/dump_modify.rst
View File

@ -17,7 +17,7 @@ Syntax
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *types* or *units* or *unwrap*
.. parsed-literal::
@ -74,12 +74,14 @@ Syntax
-N = sort per-atom lines in descending order by the Nth column
*tfactor* arg = time scaling factor (> 0.0)
*thermo* arg = *yes* or *no*
*time* arg = *yes* or *no*
*thresh* args = attribute operator value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding
*time* arg = *yes* or *no*
*triclinic/general* arg = *yes* or *no*
*types* value = *numeric* or *labels*
*units* arg = *yes* or *no*
*unwrap* arg = *yes* or *no*
@ -802,8 +804,9 @@ region since the last dump.
dump_modify ... thresh v_charge |^ LAST
This will dump atoms whose charge has changed from an absolute value
less than :math:`\frac12` to greater than :math:`\frac12` (or vice versa) since the last dump (e.g., due to reactions and subsequent charge equilibration in a
reactive force field).
less than :math:`\frac12` to greater than :math:`\frac12` (or vice
versa) since the last dump (e.g., due to reactions and subsequent
charge equilibration in a reactive force field).
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "\|\^".
@ -811,6 +814,18 @@ In this context, XOR means that if either the attribute or value is
0.0 and the other is non-zero, then the result is "true" and the
threshold criterion is met. Otherwise it is not met.
.. note::
For style *custom*, the *triclinic/general* keyword can alter dump
output for general triclinic simulation boxes and their atoms. See
the :doc:`dump <dump>` command for details of how this changes the
format of dump file snapshots. The thresh keyword may access
per-atom attributes either directly or indirectly through a compute
or variable. If the attribute is an atom coordinate or a per-atom
vector (such as velocity, force, or dipole moment), its value will
*NOT* be a general triclinic (rotated) value. Rather it will be a
restricted triclinic value.
----------
The *time* keyword only applies to the dump *atom*, *custom*, *local*,
@ -835,6 +850,36 @@ The default setting is *no*\ .
----------
The *types* keyword applies only to the dump xyz style. If this keyword is
used with a value of *numeric*, then numeric atom types are printed in the
xyz file (default). If the value *labels* is specified, then
:doc:`type labels <Howto_type_labels>` are printed for atom types.
----------
The *triclinic/general* keyword only applies to the dump *atom* and
*custom* styles. It can only be used with a value of *yes* if the
simulation box was created as a general triclinic box. See the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
explanation of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
If this keyword is used with a value of *yes*, the box information at
the beginning of each snapshot will include information about the 3
arbitrary edge vectors **A**, **B**, **C** that define the general
triclinic box as well as their origin. The format is described on the
:doc:`dump <dump>` doc page.
The coordinates of each atom will likewise be output as values in (or
near) the general triclinic box. Likewise, per-atom vector quantities
such as velocity, omega, dipole moment, etc will have orientations
consistent with the general triclinic box, meaning they will be
rotated relative to the standard xyz coordinate axes. See the
:doc:`dump <dump>` doc page for a full list of which dump attributes
this affects.
----------
The *units* keyword only applies to the dump *atom*, *custom*, and
*local* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump
@ -922,10 +967,12 @@ The option defaults are
* sort = off for dump styles *atom*, *custom*, *cfg*, and *local*
* sort = id for dump styles *dcd*, *xtc*, and *xyz*
* thresh = none
* time = no
* triclinic/general = no
* types = numeric
* units = no
* unwrap = no
* compression_level = 9 (gz variants)
* compression_level = 0 (zstd variants)
* checksum = yes (zstd variants)

2
doc/src/fix.rst
View File

@ -226,6 +226,7 @@ accelerated styles exist.
* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
* :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations
* :doc:`deform <fix_deform>` - change the simulation box size/shape
* :doc:`deform/pressure <fix_deform_pressure>` - change the simulation box size/shape with additional loading conditions
* :doc:`deposit <fix_deposit>` - add new atoms above a surface
* :doc:`dpd/energy <fix_dpd_energy>` - constant energy dissipative particle dynamics
* :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
@ -431,6 +432,7 @@ accelerated styles exist.
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
* :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
* :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
* :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
* :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
* :doc:`wall/harmonic <fix_wall>` - harmonic spring wall

24
doc/src/fix_adapt.rst
View File

@ -21,17 +21,17 @@ Syntax
*pair* args = pstyle pparam I J v_name
pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
I,J = type pair(s) to set parameter for (integer or type label)
v_name = variable with name that calculates value of pparam
*bond* args = bstyle bparam I v_name
bstyle = bond style name (e.g., harmonic)
bparam = parameter to adapt over time
I = type bond to set parameter for
I = type bond to set parameter for (integer or type label)
v_name = variable with name that calculates value of bparam
*angle* args = astyle aparam I v_name
astyle = angle style name (e.g., harmonic)
aparam = parameter to adapt over time
I = type angle to set parameter for
I = type angle to set parameter for (integer or type label)
v_name = variable with name that calculates value of aparam
*kspace* arg = v_name
v_name = variable with name that calculates scale factor on :math:`k`-space terms
@ -67,6 +67,9 @@ Examples
variable ramp_up equal "ramp(0.01,0.5)"
fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up
labelmap atom 1 c1
fix 1 all adapt 1 pair soft a c1 c1 v_prefactor
Description
"""""""""""
@ -254,10 +257,12 @@ should be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the :math:`I` and :math:`J` settings still need to be
specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
can be specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric :math:`J,I` interaction to the same values.
Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and
:math:`J` can be specified in one of several ways. Explicit numeric values
can be used for each, as in the first example above. Or, one or both of
the types in the I,J pair can be a :doc:`type label <Howto_type_labels>`.
LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to
the same values.
A wild-card asterisk can be used in place of or in conjunction with
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
@ -266,8 +271,9 @@ is the number of atom types, then an asterisk with no numeric values
means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where :math:`J < I`, they are ignored.
(inclusive). For the asterisk syntax, note that only type pairs with
:math:`I \le J` are considered; if asterisks imply type pairs where
:math:`J < I`, they are ignored.
IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
<pair_hybrid>` is being used, then the *pstyle* will be a sub-style

22
doc/src/fix_adapt_fep.rst
View File

@ -21,13 +21,13 @@ Syntax
*pair* args = pstyle pparam I J v_name
pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
I,J = type pair(s) to set parameter for (integer or type label)
v_name = variable with name that calculates value of pparam
*kspace* arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
*atom* args = aparam v_name
aparam = parameter to adapt over time
I = type(s) to set parameter for
I = type(s) to set parameter for (integer or type label)
v_name = variable with name that calculates value of aparam
* zero or more keyword/value pairs may be appended
@ -56,6 +56,9 @@ Examples
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
labelmap atom 1 c1
fix 1 all adapt/fep 1 pair soft a c1 c1 v_prefactor
Example input scripts available: examples/PACKAGES/fep
@ -218,10 +221,12 @@ be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the *I* and *J* settings still need to be
specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and
:math:`J` can be specified in one of several ways. Explicit numeric values
can be used for each, as in the first example above. Or, one or both of
the types in the I,J pair can be a :doc:`type label <Howto_type_labels>`.
LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to
the same values.
A wild-card asterisk can be used in place of or in conjunction with
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
@ -230,8 +235,9 @@ the number of atom types, then an asterisk with no numeric values means
all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where :math:`J < I`, they are ignored.
(inclusive). For the asterisk syntax, note that only type pairs with
:math:`I \le J` are considered; if asterisks imply type pairs where
:math:`J < I`, they are ignored.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is
being used, then the *pstyle* will be a sub-style name. You must specify

23
doc/src/fix_amoeba_bitorsion.rst
View File

@ -35,7 +35,11 @@ the implementation of AMOEBA and HIPPO in LAMMPS.
Bitorsion interactions add additional potential energy contributions
to pairs of overlapping phi-psi dihedrals of amino-acids, which are
important to properly represent their conformational behavior.
important to properly represent their conformational behavior. Each
bitorsion interaction is thus defined for a 5-tuple of atoms
:math:`IJKLM` with bonds between successive atoms in the list,
i.e. two overlapping dihedral interactions for atoms :math:`IJKL` and
:math:`JKLM`.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/bitorsion
@ -68,14 +72,15 @@ lines:
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to :math:`N` to enumerate the bitorsion
5-atom tuples; it is ignored by LAMMPS. The second column is the
*type* of the interaction; it is an index into the bitorsion force
field file. The remaining 5 columns are the atom IDs of the atoms in
the two 4-atom dihedrals that overlap to create the bitorsion 5-body
interaction. Note that the *bitorsions* and *BiTorsions* keywords for
the header and body sections match those specified in the
:doc:`read_data <read_data>` command following the data file name.
The first column is an index from 1 to :math:`N` to enumerate the
bitorsion 5-atom tuples; it is ignored by LAMMPS. The second column
is the *type* of the interaction; it is an index into the bitorsion
force field file. The remaining 5 columns are the atom IDs of the
atoms (in order) for the 5-tuple :math:`IJKLM`, as described above.
Note that the *bitorsions* and *BiTorsions* keywords for the header
and body sections match those specified in the :doc:`read_data
<read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS

23
doc/src/fix_amoeba_pitorsion.rst
View File

@ -57,7 +57,7 @@ should have two lines like these in its header section:
M pitorsion types
N pitorsions
where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
where :math:`N` is the number of pitorsion 6-body interactions and :math:`M` is
the number of pitorsion types. It should also have two sections in the body
of the data file like these with :math:`M` and :math:`N` lines each:
@ -74,21 +74,20 @@ of the data file like these with :math:`M` and :math:`N` lines each:
PiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
1 1 2 4 3 20 21 24
2 5 21 23 22 37 38 41
[...]
N 3 314 315 317 318 330
N 7 27 29 28 30 35 36
For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
enumerate the pitorsion types. The second column is the single
For PiTorsion Coeffs, the first column is an index from 1 to :math:`M`
to enumerate the pitorsion types. The second column is the single
prefactor coefficient needed for each type.
For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
column is the "type" of the interaction; it is an index into the
PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
atoms in the two 4-atom dihedrals that overlap to create the pitorsion
5-body interaction.
For PiTorsions, the first column is an index from 1 to :math:`N` to
enumerate the pitorsion 6-atom tuples; it is ignored by LAMMPS. The
second column is the "type" of the interaction; it is an index into
the PiTorsion Coeffs. The remaining 6 columns are the atom IDs of the
atoms (in order) for the 6-tuple :math:`IJKLMN`, as described above.
Note that the *pitorsion types* and *pitorsions* and *PiTorsion
Coeffs* and *PiTorsions* keywords for the header and body sections of

4
doc/src/fix_atom_swap.rst
View File

@ -21,7 +21,7 @@ Syntax
.. parsed-literal::
*types* values = two or more atom types
*types* values = two or more atom types (1-Ntypes or type label)
*mu* values = chemical potential of swap types (energy units)
*ke* value = *no* or *yes*
*no* = no conservation of kinetic energy after atom swaps
@ -168,7 +168,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "intensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during

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