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Merge branch 'develop' of github.com:lammps/lammps into ave_histo_vector_bug

Browse Source
This commit is contained in:
Germain Clavier
2024-04-20 17:38:38 +02:00
parent 38c7d7aa1c 6836bca5f8
commit baaea8271b
1873 changed files with 99400 additions and 53846 deletions
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7
.github/CODEOWNERS vendored
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@ -37,7 +37,7 @@ 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/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -65,9 +65,12 @@ 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
# core LAMMPS classes
@ -80,7 +83,7 @@ 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.*') }}

2
.github/workflows/unittest-macos.yml vendored
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@ -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 }}

78
cmake/CMakeLists.txt
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@ -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 ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@ -415,6 +432,7 @@ if(BUILD_OMP)
(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@ -425,6 +443,21 @@ if(BUILD_OMP)
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${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_${BTYPE} -fopenmp")
endif()
endif()
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
@ -539,12 +572,12 @@ endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
foreach(HEADER cmath)
check_include_file_cxx(${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")
@ -971,14 +1004,15 @@ 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()
@ -997,28 +1031,10 @@ 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")
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 "Using builtin distributed FFT algorithms")
endif()
if(PKG_KOKKOS)
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-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" 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)

7
cmake/Modules/Packages/GPU.cmake
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@ -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})

38
cmake/Modules/Packages/KOKKOS.cmake
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@ -16,11 +16,6 @@ endif()
if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
# NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
########################################################################
@ -50,8 +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/4.3.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "889dcea2b5ced3debdc5b0820044bdc4" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -76,7 +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 4.3.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -131,16 +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}

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

@ -21,9 +21,9 @@ 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"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

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)

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

4
doc/src/Commands_bond.rst
View File

@ -89,6 +89,7 @@ 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>`
@ -124,9 +125,10 @@ 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>`
@ -262,6 +263,7 @@ 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>`

4
doc/src/Commands_pair.rst
View File

@ -146,7 +146,7 @@ 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 +245,7 @@ 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 +257,7 @@ 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:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

2
doc/src/Commands_removed.rst
View File

@ -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

113
doc/src/Developer_updating.rst
View File

@ -18,8 +18,10 @@ 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`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
@ -129,6 +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()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -136,11 +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:
@ -196,6 +234,71 @@ New:
fp = utils::open_potential(filename, lmp);
Use symbolic Atom and AtomVec constants instead of numerical values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
Properties in LAMMPS that were represented by integer values (0, 1,
2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
classes derived from it) (and its derived classes) have been converted
to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
Old:
.. code-block:: c++
molecular = 0;
mass_type = 1;
if (atom->molecular == 2)
if (atom->map_style == 2)
atom->add_callback(0);
atom->delete_callback(id,1);
New:
.. code-block:: c++
molecular = Atom::ATOMIC;
mass_type = AtomVec::PER_TYPE;
if (atom->molecular == Atom::TEMPLATE)
if (atom->map_style == Atom::MAP_HASH)
atom->add_callback(Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

4
doc/src/Developer_utils.rst
View File

@ -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.

49
doc/src/Fortran.rst
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@ -315,6 +315,10 @@ 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 +1255,8 @@ 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 +1402,28 @@ 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 +1431,23 @@ 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`
--------

124
doc/src/Howto_2d.rst
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@ -1,42 +1,112 @@
2d simulations
==============
================
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

2
doc/src/Howto_cmake.rst
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@ -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
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@ -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
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@ -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
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@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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

33
doc/src/Modify_style.rst
View File

@ -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)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

17
doc/src/Python_scatter.rst
View File

@ -54,8 +54,21 @@ like this:
x[3] = x coord of atom with ID 2
...
x[n3-1] = z coord of atom with ID natoms
lmp.scatter_atoms("x",1,3,x)
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.

64
doc/src/Speed_kokkos.rst
View File

@ -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
@ -54,22 +71,22 @@ produce an executable compatible with a specific hardware.
:class: note
Kokkos with CUDA currently implicitly assumes that the MPI library is
GPU-aware. This is not always the case, especially when using
GPU-aware. This is not always the case, especially when using
pre-compiled MPI libraries provided by a Linux distribution. This is
not a problem when using only a single GPU with a single MPI
rank. When running with multiple MPI ranks, you may see segmentation
rank. When running with multiple MPI ranks, you may see segmentation
faults without GPU-aware MPI support. These can be avoided by adding
the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
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::
@ -416,15 +443,22 @@ Generally speaking, the following rules of thumb apply:
performance of a KOKKOS style is a bit slower than the OPENMP
package.
* When running large number of atoms per GPU, KOKKOS is typically faster
than the GPU package when compiled for double precision. The benefit
than the GPU package when compiled for double precision. The benefit
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

4
doc/src/angle_charmm.rst
View File

@ -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).

19
doc/src/angle_lepton.rst
View File

@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
angle_style lepton
angle_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
angle_style lepton
angle_style lepton no_offset
angle_coeff 1 120.0 "k*theta^2; k=250.0"
angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@ -41,6 +51,13 @@ 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:: 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
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an

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

615
doc/src/atom_style.rst
View File

@ -49,248 +49,221 @@ 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 |
+--------------+-----------------------------------------------------+--------------------------------------+
| *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
* - *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
@ -309,6 +282,149 @@ 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.
@ -326,11 +442,12 @@ dipole". When a hybrid style is used, atoms store and communicate the
union of all quantities implied by the individual styles.
When using the *hybrid* style, you cannot combine the *template* style
with another molecular style that stores bond,angle,etc info on a
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>`.
----------
@ -346,54 +463,20 @@ 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.
----------

4
doc/src/bond_bpm_rotational.rst
View File

@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

4
doc/src/bond_bpm_spring.rst
View File

@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

19
doc/src/bond_lepton.rst
View File

@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
bond_style lepton
bond_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
bond_style lepton
bond_style lepton no_offset
bond_coeff 1 1.5 "k*r^2; k=250.0"
bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@ -40,6 +50,13 @@ 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:: 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
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical

54
doc/src/boundary.rst
View File

@ -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
View File

@ -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
""""""""""""""""

2
doc/src/compute_efield_wolf_atom.rst
View File

@ -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
doc/src/compute_fabric.rst
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
View File

@ -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
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@ -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
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@ -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``
----------

5
doc/src/compute_property_atom.rst
View File

@ -23,8 +23,9 @@ Syntax
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
temperature, heatflow,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
shapex, shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
@ -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
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@ -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

37
doc/src/compute_rdf.rst
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@ -176,22 +176,29 @@ 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
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@ -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``
----------

7
doc/src/compute_stress_mop.rst
View File

@ -132,10 +132,13 @@ 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
""""""""""""""""

253
doc/src/create_atoms.rst
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@ -86,25 +86,46 @@ 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 +147,117 @@ 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 +317,6 @@ 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 +329,12 @@ 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
@ -463,12 +530,19 @@ 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 +610,11 @@ 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.
----------

7
doc/src/dihedral_charmm.rst
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@ -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

111
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]
@ -131,8 +130,6 @@ 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 +275,20 @@ 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 +305,10 @@ 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 +330,10 @@ 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 +405,6 @@ command.
Dump files in other popular formats:
.. note::
This section only discusses file formats relevant to this doc page.
@ -656,6 +660,87 @@ 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

47
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 *units* or *unwrap*
.. parsed-literal::
@ -74,12 +74,13 @@ 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*
*units* arg = *yes* or *no*
*unwrap* arg = *yes* or *no*
@ -802,8 +803,9 @@ 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 +813,18 @@ 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 +849,29 @@ The default setting is *no*\ .
----------
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
@ -922,6 +959,8 @@ 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
* units = no
* unwrap = no

2
doc/src/fix.rst
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@ -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
@ -427,6 +428,7 @@ 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

28
doc/src/fix_ave_chunk.rst
View File

@ -31,7 +31,7 @@ Syntax
v_name = per-atom vector calculated by an atom-style variable with name
* zero or more keyword/arg pairs may be appended
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *append* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -51,6 +51,8 @@ Syntax
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
*file* arg = filename
filename = file to write results to
*append* arg = filename
filename = file to append results to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -433,15 +435,21 @@ molecule.
----------
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
text file in the following format. A line with the timestep and number of
chunks is written. Then one line per chunk is written, containing the chunk
ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of atoms
in the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every :math:`N_\text{freq}`
timesteps, a section of chunk info will be written to a text file in the
following format. A line with the timestep and number of chunks is
written. Then one line per chunk is written, containing the chunk ID
:math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of
atoms in the chunk, and one or more calculated values. More explanation
of the optional values is given below. The number of values in each
line corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
quantities, as explained above.

1
doc/src/fix_ave_correlate.rst
View File

@ -65,7 +65,6 @@ Examples
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
Description

13
doc/src/fix_ave_correlate_long.rst
View File

@ -20,11 +20,11 @@ Syntax
.. parsed-literal::
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = global value calculated by an equal-style variable with name
v_name[I] = Ith component of global vector calculated by a vector-style variable with name
v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
@ -63,6 +63,7 @@ Examples
fix 1 all ave/correlate/long 1 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper title1 "My correlation data" nlen 15 ncount 3
fix 1 all ave/correlate/long 1 10000 c_thermo_press[*]
Description
"""""""""""
@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a compute or fix or the
evaluation of an equal-style variable. See the
:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
evaluation of an equal-style or vector-style variable. For
vector-style variables, the specified indices can include a wildcard
character. See the :doc:`fix ave/correlate <fix_ave_correlate>` page
for details.
The *Nevery* and *Nfreq* arguments specify on what time steps the input
values will be used to calculate correlation data and the frequency

36
doc/src/fix_ave_histo.rst
View File

@ -35,7 +35,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
* keyword = *mode* or *kind* or *file* or *append* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
*kind* arg = *global* or *peratom* or *local*
*file* arg = filename
filename = name of file to output histogram(s) to
*append* arg = filename
filename = name of file to append histogram(s) to
*ave* args = *one* or *running* or *window*
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
@ -317,19 +319,25 @@ on. The default is step 0. Often input values can be 0.0 at time 0,
so setting *start* to a larger value can avoid including a 0.0 in
a running or windowed histogram.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one histogram is written to the file. This includes a leading
line that contains the timestep, number of bins, the total count of
values contributing to the histogram, the count of values that were
not histogrammed (see the *beyond* keyword), the minimum value
encountered, and the maximum value encountered. The min/max values
include values that were not histogrammed. Following the leading
line, one line per bin is written into the file. Each line contains
the bin #, the coordinate for the center of the bin (between *lo* and
*hi*\ ), the count of values in the bin, and the normalized count. The
normalized count is the bin count divided by the total count (not
including values not histogrammed), so that the normalized values sum
to 1.0 across all bins.
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
histogram is written to the file. This includes a leading line that
contains the timestep, number of bins, the total count of values
contributing to the histogram, the count of values that were not
histogrammed (see the *beyond* keyword), the minimum value encountered,
and the maximum value encountered. The min/max values include values
that were not histogrammed. Following the leading line, one line per
bin is written into the file. Each line contains the bin #, the
coordinate for the center of the bin (between *lo* and *hi*\ ), the
count of values in the bin, and the normalized count. The normalized
count is the bin count divided by the total count (not including values
not histogrammed), so that the normalized values sum to 1.0 across all
bins.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of

29
doc/src/fix_ave_time.rst
View File

@ -28,7 +28,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *mode* or *file* or *append* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
M = value # from 1 to Nvalues
*file* arg = filename
filename = name of file to output time averages to
*append* arg = filename
filename = name of file to append time averages to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -270,16 +272,21 @@ are effectively constant or are simply current values (e.g., they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output).
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For *mode* =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For *mode* = vector, an array
of numbers is written each time output is performed. The number of rows
is the length of the input vectors, and the number of columns is the
number of values. Thus the file ends up to be a series of these array
sections.
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
quantity or vector of quantities is written to the file for each input
value specified in the fix ave/time command. For *mode* = scalar, this
means a single line is written each time output is performed. Thus the
file ends up to be a series of lines, i.e. one column of numbers for
each input value. For *mode* = vector, an array of numbers is written
each time output is performed. The number of rows is the length of the
input vectors, and the number of columns is the number of values. Thus
the file ends up to be a series of these array sections.
.. versionadded:: 4May2022

13
doc/src/fix_balance.rst
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@ -14,15 +14,15 @@ Syntax
* balance = style name of this fix command
* Nfreq = perform dynamic load balancing every this many steps
* thresh = imbalance threshold that must be exceeded to perform a re-balance
* style = *shift* or *rcb*
* style = *shift* or *rcb* or *report*
.. parsed-literal::
shift args = dimstr Niter stopthresh
*shift* args = dimstr Niter stopthresh
dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshold is reached
*rcb* args = none
*report* args = none
* zero or more keyword/arg pairs may be appended
* keyword = *weight* or *out*
@ -70,6 +70,13 @@ re-balancing is performed periodically during the simulation. To
perform "static" balancing, before or between runs, see the
:doc:`balance <balance>` command.
.. versionadded:: 17Apr2024
The *report* balance style only computes the load imbalance but
does not attempt any re-balancing. This way the load imbalance
information can be used otherwise, for instance for stopping a
run with :doc:`fix halt <fix_halt>`.
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
where the computational cost varies significantly between different

10
doc/src/fix_charge_regulation.rst
View File

@ -253,11 +253,11 @@ built with that package. See the :doc:`Build package <Build_package>`
page for more info.
The :doc:`atom_style <atom_style>`, used must contain the charge
property, for example, the style could be *charge* or *full*. Only
usable for 3D simulations. Atoms specified as free ions cannot be part
of rigid bodies or molecules and cannot have bonding interactions. The
scheme is limited to integer charges, any atoms with non-integer charges
will not be considered by the fix.
property and have per atom type masses, for example, the style could be
*charge* or *full*. Only usable for 3D simulations. Atoms specified as
free ions cannot be part of rigid bodies or molecules and cannot have
bonding interactions. The scheme is limited to integer charges, any
atoms with non-integer charges will not be considered by the fix.
All interaction potentials used must be continuous, otherwise the MD
integration and the particle exchange MC moves do not correspond to the

181
doc/src/fix_deform.rst
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@ -4,6 +4,9 @@
fix deform command
==================
:doc:`fix deform/pressure <fix_deform_pressure>` command
========================================================
Accelerator Variants: *deform/kk*
Syntax
@ -11,18 +14,18 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID deform N parameter args ... keyword value ...
fix ID group-ID fix_style N parameter style args ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* deform = style name of this fix command
* fix_style = *deform* or *deform/pressure*
* N = perform box deformation every this many timesteps
* one or more parameter/arg pairs may be appended
* one or more parameter/style/args sequences of arguments may be appended
.. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
*x*, *y*, *z* args = style value(s)
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
*final* values = lo hi
lo hi = box boundaries at end of run (distance units)
*delta* values = dlo dhi
@ -43,8 +46,15 @@ Syntax
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle*
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
*final* value = tilt
tilt = tilt factor at end of run (distance units)
*delta* value = dtilt
@ -62,9 +72,12 @@ Syntax
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
* zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units*
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
.. parsed-literal::
@ -77,6 +90,15 @@ Syntax
*units* value = *lattice* or *box*
lattice = distances are defined in lattice units
box = distances are defined in simulation box units
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
Examples
""""""""
@ -88,6 +110,8 @@ Examples
fix 1 all deform 1 xy erate 0.001 remap v
fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
Description
"""""""""""
@ -95,29 +119,46 @@ Change the volume and/or shape of the simulation box during a dynamics
run. Orthogonal simulation boxes have 3 adjustable parameters
(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously by this command.
adjusted independently and simultaneously.
This fix can be used to perform non-equilibrium MD (NEMD) simulations
of a continuously strained system. See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
The fix deform command allows use of all the arguments listed above,
except those flagged as available ONLY for the :doc:`fix
deform/pressure <fix_deform_pressure>` command, which are
pressure-based controls. The fix deform/pressure command allows use
of all the arguments listed above.
The rest of this doc page explains the options common to both
commands. The :doc:`fix deform/pressure <fix_deform_pressure>` doc
page explains the options available ONLY with the fix deform/pressure
command. Note that a simulation can define only a single deformation
command: fix deform or fix deform/pressure.
Both these fixes can be used to perform non-equilibrium MD (NEMD)
simulations of a continuously strained system. See the :doc:`fix
nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform
<compute_temp_deform>` commands for more details. Note that
simulation of a continuously extended system (extensional flow) can be
modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
commands <fix_nh_uef>`.
For the *x*, *y*, *z* parameters, the associated dimension cannot be
shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated
second dimension cannot be shrink-wrapped. Dimensions not varied by this
command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
second dimension cannot be shrink-wrapped. Dimensions not varied by
this command can be periodic or non-periodic. Dimensions
corresponding to unspecified parameters can also be controlled by a
:doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
The size and shape of the simulation box at the beginning of the
simulation run were either specified by the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` command used to setup the simulation
initially if it is the first run, or they are the values from the end
of the previous run. The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If
fix deform changes the xy,xz,yz tilt factors, then the simulation box
must be triclinic, even if its initial tilt factors are 0.0.
simulation run were either specified by the :doc:`create_box
<create_box>` or :doc:`read_data <read_data>` or :doc:`read_restart
<read_restart>` command used to setup the simulation initially if it
is the first run, or they are the values from the end of the previous
run. The :doc:`create_box <create_box>`, :doc:`read data
<read_data>`, and :doc:`read_restart <read_restart>` commands specify
whether the simulation box is orthogonal or non-orthogonal (triclinic)
and explain the meaning of the xy,xz,yz tilt factors. If fix deform
changes the xy,xz,yz tilt factors, then the simulation box must be
triclinic, even if its initial tilt factors are 0.0.
As described below, the desired simulation box size and shape at the
end of the run are determined by the parameters of the fix deform
@ -258,21 +299,22 @@ of the units keyword below.
The *variable* style changes the specified box length dimension by
evaluating a variable, which presumably is a function of time. The
variable with *name1* must be an :doc:`equal-style variable <variable>`
and should calculate a change in box length in units of distance.
Note that this distance is in box units, not lattice units; see the
discussion of the *units* keyword below. The formula associated with
variable *name1* can reference the current timestep. Note that it
should return the "change" in box length, not the absolute box length.
This means it should evaluate to 0.0 when invoked on the initial
timestep of the run following the definition of fix deform. It should
evaluate to a value > 0.0 to dilate the box at future times, or a
value < 0.0 to compress the box.
variable with *name1* must be an :doc:`equal-style variable
<variable>` and should calculate a change in box length in units of
distance. Note that this distance is in box units, not lattice units;
see the discussion of the *units* keyword below. The formula
associated with variable *name1* can reference the current timestep.
Note that it should return the "change" in box length, not the
absolute box length. This means it should evaluate to 0.0 when
invoked on the initial timestep of the run following the definition of
fix deform. It should evaluate to a value > 0.0 to dilate the box at
future times, or a value < 0.0 to compress the box.
The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of box length
change, in units of distance/time, i.e. the time-derivative of the
*name1* variable. This quantity is used internally by LAMMPS to reset
atom velocities when they cross periodic boundaries. It is computed
The variable *name2* must also be an :doc:`equal-style variable
<variable>` and should calculate the rate of box length change, in
units of distance/time, i.e. the time-derivative of the *name1*
variable. This quantity is used internally by LAMMPS to reset atom
velocities when they cross periodic boundaries. It is computed
internally for the other styles, but you must provide it when using an
arbitrary variable.
@ -414,12 +456,13 @@ can reference the current timestep. Note that it should return the
should evaluate to 0.0 when invoked on the initial timestep of the run
following the definition of fix deform.
The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of tilt change,
in units of distance/time, i.e. the time-derivative of the *name1*
variable. This quantity is used internally by LAMMPS to reset atom
velocities when they cross periodic boundaries. It is computed
internally for the other styles, but you must provide it when using an
arbitrary variable.
The variable *name2* must also be an :doc:`equal-style variable
<variable>` and should calculate the rate of tilt change, in units of
distance/time, i.e. the time-derivative of the *name1* variable. This
quantity is used internally by LAMMPS to reset atom velocities when
they cross periodic boundaries. It is computed internally for the
other styles, but you must provide it when using an arbitrary
variable.
Here is an example of using the *variable* style to perform the same
box deformation as the *wiggle* style formula listed above, where we
@ -510,33 +553,40 @@ box without explicit remapping of their coordinates.
.. note::
For non-equilibrium MD (NEMD) simulations using "remap v" it is
usually desirable that the fluid (or flowing material, e.g. granular
particles) stream with a velocity profile consistent with the
deforming box. As mentioned above, using a thermostat such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin <fix_langevin>`
(with a bias provided by :doc:`compute temp/deform <compute_temp_deform>`), will typically accomplish
that. If you do not use a thermostat, then there is no driving force
pushing the atoms to flow in a manner consistent with the deforming
box. E.g. for a shearing system the box deformation velocity may vary
usually desirable that the fluid (or flowing material,
e.g. granular particles) stream with a velocity profile consistent
with the deforming box. As mentioned above, using a thermostat
such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin
<fix_langevin>` (with a bias provided by :doc:`compute temp/deform
<compute_temp_deform>`), will typically accomplish that. If you do
not use a thermostat, then there is no driving force pushing the
atoms to flow in a manner consistent with the deforming box.
E.g. for a shearing system the box deformation velocity may vary
from 0 at the bottom to 10 at the top of the box. But the stream
velocity profile of the atoms may vary from -5 at the bottom to +5 at
the top. You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands. One way to induce
atoms to stream consistent with the box deformation is to give them an
velocity profile of the atoms may vary from -5 at the bottom to +5
at the top. You can monitor these effects using the :doc:`fix
ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform
<compute_temp_deform>`, and :doc:`compute temp/profile
<compute_temp_profile>` commands. One way to induce atoms to
stream consistent with the box deformation is to give them an
initial velocity profile, via the :doc:`velocity ramp <velocity>`
command, that matches the box deformation rate. This also typically
helps the system come to equilibrium more quickly, even if a
thermostat is used.
command, that matches the box deformation rate. This also
typically helps the system come to equilibrium more quickly, even
if a thermostat is used.
.. note::
If a :doc:`fix rigid <fix_rigid>` is defined for rigid bodies, and
*remap* is set to *x*, then the center-of-mass coordinates of rigid
bodies will be remapped to the changing simulation box. This will be
done regardless of whether atoms in the rigid bodies are in the fix
deform group or not. The velocity of the centers of mass are not
remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod <fix_nvt_sllod>` does not currently do anything special
bodies will be remapped to the changing simulation box. This will
be done regardless of whether atoms in the rigid bodies are in the
fix deform group or not. The velocity of the centers of mass are
not remapped even if *remap* is set to *v*, since :doc:`fix
nvt/sllod <fix_nvt_sllod>` does not currently do anything special
for rigid particles. If you wish to perform a NEMD simulation of
rigid particles, you can either thermostat them independently or
include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod <fix_nvt_sllod>`.
include a background fluid and thermostat the fluid via :doc:`fix
nvt/sllod <fix_nvt_sllod>`.
The *flip* keyword allows the tilt factors for a triclinic box to
exceed half the distance of the parallel box length, as discussed
@ -568,7 +618,8 @@ command if you want to include lattice spacings in a variable formula.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
This fix will restore the initial box settings from :doc:`binary
restart files <restart>`, which allows the fix to be properly continue
deformation, when using the start/stop options of the :doc:`run <run>`
command. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
@ -586,12 +637,14 @@ Restrictions
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y in
xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y
in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
command.
Related commands
""""""""""""""""
:doc:`fix deform/pressure <fix_deform_pressure>`,
:doc:`change_box <change_box>`
Default

319
doc/src/fix_deform_pressure.rst Normal file
View File

@ -0,0 +1,319 @@
.. index:: fix deform/pressure
fix deform/pressure command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID deform/pressure N parameter style args ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* deform/pressure = style name of this fix command
* N = perform box deformation every this many timesteps
* one or more parameter/arg sequences may be appended
.. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
*x*, *y*, *z* args = style value(s)
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure*
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*box* = style value
style = *volume* or *pressure*
*volume* value = none = isotropically adjust system to preserve volume of system
*pressure* values = target gain
target = target mean pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
* zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
.. parsed-literal::
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no*
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate*
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no*
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all deform/pressure 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001
fix 1 all deform/pressure 1 x trate 0.1 y volume z volume vol/balance/p yes
fix 1 all deform/pressure 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0
Description
"""""""""""
.. versionadded:: 17Apr2024
This fix is an extension of the :doc:`fix deform <fix_deform>`
command, which allows all of its options to be used as well as new
pressure-based controls implemented by this command.
All arguments described on the :doc:`fix deform <fix_deform>` doc page
also apply to this fix unless otherwise noted below. The rest of this
doc page explains the arguments specific to this fix. Note that a
simulation can define only a single deformation command: fix deform or
fix deform/pressure.
----------
For the *x*, *y*, and *z* parameters, this is the meaning of the
styles and values provided by this fix.
The *pressure* style adjusts a dimension's box length to control the
corresponding component of the pressure tensor. This option attempts to
maintain a specified target pressure using a linear controller where the
box length :math:`L` evolves according to the equation
.. math::
\frac{d L(t)}{dt} = L(t) k (P_t - P)
where :math:`k` is a proportional gain constant, :math:`P_t` is the target
pressure, and :math:`P` is the current pressure along that dimension. This
approach is similar to the method used to control the pressure by
:doc:`fix press/berendsen <fix_press_berendsen>`. The target pressure
accepts either a constant numeric value or a LAMMPS :ref:`variable <variable>`.
Notably, this variable can be a function of time or other components of
the pressure tensor. By default, :math:`k` has units of 1/(time * pressure)
although this will change if the *normalize/pressure* option is set as
:ref:`discussed below <deform_normalize>`. There is no proven method
to choosing an appropriate value of :math:`k` as it will depend on the
specific details of a simulation. Testing different values is recommended.
By default, there is no limit on the resulting strain rate in any dimension.
A maximum limit can be applied using the :ref:`max/rate <deform_max_rate>`
option. Akin to :doc:`fix nh <fix_nh>`, pressures in different dimensions
can be coupled using the :ref:`couple <deform_couple>` option. This means
the instantaneous pressure along coupled dimensions are averaged and the box
strains identically along the coupled dimensions.
The *pressure/mean* style changes a dimension's box length to maintain
a constant mean pressure defined as the trace of the pressure tensor.
This option has identical arguments to the *pressure* style and a similar
functional equation, except the current and target pressures refer to the
mean trace of the pressure tensor. All options for the *pressure* style
also apply to the *pressure/mean* style except for the
:ref:`couple <deform_couple>` option.
Note that while this style can be identical to coupled *pressure* styles,
it is generally not the same. For instance in 2D, a coupled *pressure*
style in the *x* and *y* dimensions would be equivalent to using the
*pressure/mean* style with identical settings in each dimension. However,
it would not be the same if settings (e.g. gain constants) were used in
the *x* and *y* dimensions or if the *pressure/mean* command was only applied
along one dimension.
----------
For the *xy*, *xz*, and *yz* parameters, this is the meaning of the
styles and values provided by this fix. Note that changing the
tilt factors of a triclinic box does not change its volume.
The *pressure* style adjusts a tilt factor to control the corresponding
off-diagonal component of the pressure tensor. This option attempts to
maintain a specified target value using a linear controller where the
tilt factor T evolves according to the equation
.. parsed-literal::
\frac{d T(t)}{dt} = L(t) k (P - P_t)
where :math:`k` is a proportional gain constant, :math:`P_t` is the
target pressure, :math:`P` is the current pressure, and :math:`L` is
the perpendicular box length. The target pressure accepts either a
constant numeric value or a LAMMPS :ref:`variable
<variable>`. Notably, this variable can be a function of time or other
components of the pressure tensor. By default, :math:`k` has units of
1/(time * pressure) although this will change if the
*normalize/pessure* option is set as :ref:`discussed below
<deform_normalize>`. There is no proven method to choosing an
appropriate value of :math:`k` as it will depend on the specific
details of a simulation and testing different values is
recommended. One can also apply a maximum limit to the magnitude of
the applied strain using the :ref:`max/rate <deform_max_rate>` option.
----------
The *box* parameter provides an additional control over the *x*, *y*,
and *z* box lengths by isotropically dilating or contracting the box
to either maintain a fixed mean pressure or volume. This isotropic
scaling is applied after the box is deformed by the above *x*, *y*,
*z*, *xy*, *xz*, and *yz* styles, acting as a second deformation
step. This parameter will change the overall strain rate in the *x*,
*y*, or *z* dimensions. This parameter can only be used in
combination with the *x*, *y*, or *z* commands: *vel*, *erate*,
*trate*, *pressure*, or *wiggle*. This is the meaning of its styles
and values.
The *volume* style isotropically scales box lengths to maintain a constant
box volume in response to deformation from other parameters. This style
may be useful in scenarios where one wants to apply a constant deviatoric
pressure using *pressure* styles in the *x*, *y*, and *z* dimensions (
deforming the shape of the box), while maintaining a constant volume.
The *pressure* style isotropically scales box lengths in an attempt to
maintain a target mean pressure (the trace of the pressure tensor) of the
system. This is accomplished by isotropically scaling all box lengths
:math:`L` by an additional factor of :math:`k (P_t - P_m)` where :math:`k`
is the proportional gain constant, :math:`P_t` is the target pressure, and
:math:`P_m` is the current mean pressure. This style may be useful in
scenarios where one wants to apply a constant deviatoric strain rate
using various strain-based styles (e.g. *trate*) along the *x*, *y*, and *z*
dimensions (deforming the shape of the box), while maintaining a mean pressure.
----------
The optional keywords provided by this fix are described below.
.. _deform_normalize:
The *normalize/pressure* keyword changes how box dimensions evolve when
using the *pressure* or *pressure/mean* deformation styles. If the
*deform/normalize* value is set to *yes*, then the deviation from the
target pressure is normalized by the absolute value of the target
pressure such that the proportional gain constant scales a percentage
error and has units of 1/time. If the target pressure is ever zero, this
will produce an error unless the *max/rate* keyword is defined,
described below, which will cap the divergence.
.. _deform_max_rate:
The *max/rate* keyword sets an upper threshold, *rate*, that limits the
maximum magnitude of the instantaneous strain rate applied in any dimension.
This keyword only applies to the *pressure* and *pressure/mean* options. If
a pressure-controlled rate is used for both *box* and either *x*, *y*, or
*z*, then this threshold will apply separately to each individual controller
such that the cumulative strain rate on a box dimension may be up to twice
the value of *rate*.
.. _deform_couple:
The *couple* keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together for the *pressure* option.
The value specified with the keyword determines which are coupled. For
example, *xz* means the *Pxx* and *Pzz* components of the stress tensor
are coupled. *Xyz* means all 3 diagonal components are coupled. Coupling
means two things: the instantaneous stress will be computed as an average
of the corresponding diagonal components, and the coupled box dimensions
will be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. If a *pressure*
style is defined for more than one coupled dimension, the target pressures
and gain constants must be identical. Alternatively, if a *pressure*
style is only defined for one of the coupled dimensions, its settings are
copied to other dimensions with undefined styles. *Couple xyz* can be used
for a 2d simulation; the *z* dimension is simply ignored.
.. _deform_balance:
The *vol/balance/p* keyword modifies the behavior of the *volume* style when
applied to two of the *x*, *y*, and *z* dimensions. Instead of straining
the two dimensions in lockstep, the two dimensions are allowed to
separately dilate or contract in a manner to maintain a constant
volume while simultaneously trying to keep the pressure along each
dimension equal using a method described in :ref:`(Huang2014) <Huang2014>`.
----------
If any pressure controls are used, this fix computes a temperature and
pressure each timestep. To do this, the fix creates its own computes
of style "temp" and "pressure", as if these commands had been issued:
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure
<compute_pressure>` commands for details. Note that the IDs of the
new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID =
*thermo_temp* and *thermo_press*. This means you can change the
attributes of this fix's temperature or pressure via the
:doc:`compute_modify <compute_modify>` command or print this
temperature or pressure during thermodynamic output via the
:doc:`thermo_style custom <thermo_style>` command using the
appropriate compute-ID. It also means that changing attributes of
*thermo_temp* or *thermo_press* will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix will restore the initial box settings from :doc:`binary
restart files <restart>`, which allows the fix to be properly continue
deformation, when using the start/stop options of the :doc:`run <run>`
command. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`.
If any pressure controls are used, the :doc:`fix_modify <fix_modify>`
*temp* and *press* options are supported by this fix, unlike in
:doc:`fix deform <fix_deform>`. You can use them to assign a
:doc:`compute <compute>` you have defined to this fix which will be
used in its temperature and pressure calculations. If you do this,
note that the kinetic energy derived from the compute temperature
should be consistent with the virial term computed using all atoms for
the pressure. LAMMPS will warn you if you choose to compute
temperature on a subset of atoms.
This fix can perform deformation over multiple runs, using the *start*
and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y
in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
command.
Related commands
""""""""""""""""
:doc:`fix deform <fix_deform>`, :doc:`change_box <change_box>`
Default
"""""""
The option defaults are normalize/pressure = no.
----------
.. _Huang2014:
**(Huang2014)** X. Huang, "Exploring critical-state behavior using DEM",
Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316

27
doc/src/fix_electrode.rst
View File

@ -45,7 +45,7 @@ Syntax
rng_v = integer used to initialize random number generator
* zero or more keyword/value pairs may be appended
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal* or *eta*
.. parsed-literal::
@ -68,6 +68,10 @@ Syntax
filename = file from which to read elastance matrix
*read_inv* value = filename
filename = file from which to read inverted matrix
*qtotal* value = number or *v_* equal-style variable
add overall potential so that all electrode charges add up to *qtotal*
*eta* value = d_propname
d_propname = a custom double vector defined via fix property/atom
Examples
""""""""
@ -249,6 +253,27 @@ be enabled if any electrode particle has the same type as any
electrolyte particle (which would be unusual in a typical simulation)
and the fix will issue an error in that case.
.. versionadded:: 17Apr2024
The keyword *qtotal* causes *fix electrode/conp* and *fix
electrode/thermo* to add an overall potential to all electrodes so that
the total charge on the electrodes is a specified amount (which may be
an equal-style variable). For example, if a user wanted to simulate a
solution of excess cations such that the total electrolyte charge is +2,
setting *qtotal -2* would cause the total electrode charge to be -2, so
that the simulation box remains overall electroneutral. Since *fix
electrode/conq* constrains the total charges of individual electrodes,
and since *symm on* constrains the total charge of all electrodes to be
zero, either option is incompatible with the *qtotal* keyword (even if
*qtotal* is set to zero).
.. versionadded:: 17Apr2024
The keyword *eta* takes the name of a custom double vector defined via
fix property/atom. The values will be used instead of the standard eta
value. The property/atom fix must be for vector of double values and
use the *ghost on* option.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

5
doc/src/fix_gcmc.rst
View File

@ -440,8 +440,11 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
This fix style requires an :doc:`atom style <atom_style>` with per atom
type masses.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
called. Reneighboring is **required**.
Only usable for 3D simulations.

90
doc/src/fix_indent.rst
View File

@ -8,33 +8,44 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID indent K keyword values ...
fix ID group-ID indent K gstyle args keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* indent = style name of this fix command
* K = force constant for indenter surface (force/distance\^2 units)
* one or more keyword/value pairs may be appended
* keyword = *sphere* or *cylinder* or *plane* or *side* or *units*
* gstyle = *sphere* or *cylinder* or *cone* or *plane*
.. parsed-literal::
*sphere* args = x y z R
x,y,z = position of center of indenter (distance units)
x, y, z = position of center of indenter (distance units)
R = sphere radius of indenter (distance units)
any of x,y,z,R can be a variable (see below)
any of x, y, z, R can be a variable (see below)
*cylinder* args = dim c1 c2 R
dim = *x* or *y* or *z* = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
c1, c2 = coords of cylinder axis in other 2 dimensions (distance units)
R = cylinder radius of indenter (distance units)
any of c1,c2,R can be a variable (see below)
*cone* args = dim c1 c2 radlo radhi lo hi
dim = *x* or *y* or *z* = axis of cone
c1, c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
any of c1, c2, radlo, radhi, lo, hi can be a variable (see below)
*plane* args = dim pos side
dim = *x* or *y* or *z* = plane perpendicular to this dimension
pos = position of plane in dimension x, y, or z (distance units)
pos can be a variable (see below)
side = *lo* or *hi*
* zero or more keyword/value pairs may be appended
* keyword = *side* or *units*
.. parsed-literal::
*side* value = *in* or *out*
*in* = the indenter acts on particles inside the sphere or cylinder
*out* = the indenter acts on particles outside the sphere or cylinder
*in* = the indenter acts on particles inside the sphere or cylinder or cone
*out* = the indenter acts on particles outside the sphere or cylinder or cone
*units* value = *lattice* or *box*
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
@ -53,12 +64,12 @@ Description
Insert an indenter within a simulation box. The indenter repels all
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
material or as an obstacle in a flow. Alternatively, it can be used as a
constraining wall around a simulation; see the discussion of the
*side* keyword below.
The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.
The *gstyle* geometry of the indenter can either be a sphere, a
cylinder, a cone, or a plane.
A spherical indenter exerts a force of magnitude
@ -75,15 +86,20 @@ A cylindrical indenter exerts the same force, except that *r* is the
distance from the atom to the center axis of the cylinder. The
cylinder extends infinitely along its axis.
Spherical and cylindrical indenters account for periodic boundaries in
two ways. First, the center point of a spherical indenter (x,y,z) or
axis of a cylindrical indenter (c1,c2) is remapped back into the
simulation box, if the box is periodic in a particular dimension.
This occurs every timestep if the indenter geometry is specified with
a variable (see below), e.g. it is moving over time. Second, the
calculation of distance to the indenter center or axis accounts for
periodic boundaries. Both of these mean that an indenter can
effectively move through and straddle one or more periodic boundaries.
A conical indenter is similar to a cylindrical indenter except that it
has a finite length (between *lo* and *hi*), and that two different
radii (one at each end, *radlo* and *radhi*) can be defined.
Spherical, cylindrical, and conical indenters account for periodic
boundaries in two ways. First, the center point of a spherical
indenter (x,y,z) or axis of a cylindrical/conical indenter (c1,c2) is
remapped back into the simulation box, if the box is periodic in a
particular dimension. This occurs every timestep if the indenter
geometry is specified with a variable (see below), e.g. it is moving
over time. Second, the calculation of distance to the indenter center
or axis accounts for periodic boundaries. Both of these mean that an
indenter can effectively move through and straddle one or more
periodic boundaries.
A planar indenter is really an axis-aligned infinite-extent wall
exerting the same force on atoms in the system, where *R* is the
@ -97,9 +113,13 @@ is specified as *hi*\ .
Any of the 4 quantities defining a spherical indenter's geometry can
be specified as an equal-style :doc:`variable <variable>`, namely *x*,
*y*, *z*, or *R*\ . Similarly, for a cylindrical indenter, any of *c1*,
*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be
a variable. If the value is a variable, it should be specified as
*y*, *z*, or *R*\ . For a cylindrical indenter, any of the 3
quantities *c1*, *c2*, or *R*, can be a variable. For a conical
indenter, any of the 6 quantities *c1*, *c2*, *radlo*, *radhi*, *lo*,
or *hi* can be a variable. For a planar indenter, the single value
*pos* can be a variable.
If any of these values is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to define the
indenter geometry.
@ -110,7 +130,8 @@ command keywords for the simulation box parameters and timestep and
elapsed time. Thus it is easy to specify indenter properties that
change as a function of time or span consecutive runs in a continuous
fashion. For the latter, see the *start* and *stop* keywords of the
:doc:`run <run>` command and the *elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
:doc:`run <run>` command and the *elaplong* keyword of
:doc:`thermo_style custom <thermo_style>` for details.
For example, if a spherical indenter's x-position is specified as v_x,
then this variable definition will keep it's center at a relative
@ -141,12 +162,13 @@ rate.
If the *side* keyword is specified as *out*, which is the default,
then particles outside the indenter are pushed away from its outer
surface, as described above. This only applies to spherical or
cylindrical indenters. If the *side* keyword is specified as *in*,
the action of the indenter is reversed. Particles inside the indenter
are pushed away from its inner surface. In other words, the indenter
is now a containing wall that traps the particles inside it. If the
radius shrinks over time, it will squeeze the particles.
surface, as described above. This only applies to spherical,
cylindrical, and conical indenters. If the *side* keyword is
specified as *in*, the action of the indenter is reversed. Particles
inside the indenter are pushed away from its inner surface. In other
words, the indenter is now a containing wall that traps the particles
inside it. If the radius shrinks over time, it will squeeze the
particles.
The *units* keyword determines the meaning of the distance units used
to define the indenter geometry. A *box* value selects standard
@ -166,10 +188,10 @@ lattice spacings in a variable formula.
The force constant *K* is not affected by the *units* keyword. It is
always in force/distance\^2 units where force and distance are defined
by the :doc:`units <units>` command. If you wish K to be scaled by the
lattice spacing, you can define K with a variable whose formula
contains *xlat*, *ylat*, *zlat* keywords of the
:doc:`thermo_style <thermo_style>` command, e.g.
by the :doc:`units <units>` command. If you wish K to be scaled by
the lattice spacing, you can define K with a variable whose formula
contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style
<thermo_style>` command, e.g.
.. code-block:: LAMMPS

96
doc/src/fix_neb.rst
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@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
force/distance units.
With a value of *ideal*, the spring force is computed as suggested in
ref`(WeinanE) <WeinanE>`
:ref:`(WeinanE) <WeinanE>`
.. math::
@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
equally spaced. I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
climbing replica is off, where *i* is the replica number). The
*meanDist* is the average distance between replicas. Note that in this
case the specified *Kspring* is in force units. When the climbing replica
is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
each side of the climbing image. Note that the *ideal* form of nudging
can often be more effective at keeping the replicas equally spaced before
climbing, then equally spaced either side of the climbing image whilst
climbing.
case the specified *Kspring* is in force units. When the climbing
replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
separately each side of the climbing image. Note that the *ideal* form
of nudging can often be more effective at keeping the replicas equally
spaced before climbing, then equally spaced either side of the climbing
image whilst climbing.
With a value of *equal* the spring force is computed as for *ideal*
when the climbing replica is off, promoting equidistance. When the climbing
With a value of *equal* the spring force is computed as for *ideal* when
the climbing replica is off, promoting equidistance. When the climbing
replica is on, the spring force is computed to promote equidistant
absolute differences in energy, rather than distance, each side of
the climbing image:
absolute differences in energy, rather than distance, each side of the
climbing image:
.. math::
@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
*meanEdist* is the average absolute energy difference between
replicas up to the climbing image or from the climbing image
to the final image, for images before or after the climbing
image respectively. :math:`ED_{ideal}` is the corresponding
cumulative sum of average absolute energy differences in
each case, in close analogy to *ideal*. This form of nudging
is to aid schemes which integrate forces along, or near to,
NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
*meanEdist* is the average absolute energy difference between replicas
up to the climbing image or from the climbing image to the final image,
for images before or after the climbing image
respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
average absolute energy differences in each case, in close analogy to
*ideal*. This form of nudging is to aid schemes which integrate forces
along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
----------
The keyword *perp* specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too strongly kinked. It can
The keyword *perp* specifies if and how a perpendicular nudging force is
computed. It adds a spring force perpendicular to the path in order to
prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
:ref:`(Maras) <Maras1>` for details.
resolution is poor. I.e. when few replicas are used; see :ref:`(Maras)
<Maras1>` for details.
The perpendicular spring force is given by
@ -181,10 +180,10 @@ force is added.
By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word *end*, additional
forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy E to the
target energy ETarget.
respective local minima. By using the key word *end*, additional forces
can be applied to the first and/or last replicas, to enable them to
relax toward a MEP while constraining their energy E to the target
energy ETarget.
If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
specified replica becomes:
@ -197,33 +196,33 @@ specified replica becomes:
The "spring" constant on the difference in energies is the specified
*Kspring3* value.
When *estyle* is specified as *first*, the force is applied to the
first replica. When *estyle* is specified as *last*, the force is
applied to the last replica. Note that the *end* keyword can be used
twice to add forces to both the first and last replicas.
When *estyle* is specified as *first*, the force is applied to the first
replica. When *estyle* is specified as *last*, the force is applied to
the last replica. Note that the *end* keyword can be used twice to add
forces to both the first and last replicas.
For both these *estyle* settings, the target energy *ETarget* is set
to the initial energy of the replica (at the start of the NEB
calculation).
If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
force is applied to the last replica, but the target energy *ETarget*
is continuously set to the energy of the first replica, as it evolves
force is applied to the last replica, but the target energy *ETarget* is
continuously set to the energy of the first replica, as it evolves
during the NEB relaxation.
The difference between these two *estyle* options is as follows. When
*estyle* is specified as *last/efirst*, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying *estyle* as *last/efirst/middle* which will alter the
inter-replica force applied to intermediate replicas by removing the
contribution of the gradient to the inter-replica force. This will
only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
inter-replica force applied to the intermediate replicas (neither first
or last). If the initial path is too far from the MEP, an intermediate
replica may relax "faster" and reach a lower energy than the last
replica. In this case the intermediate replica will be relaxing toward
its own local minima. This behavior can be prevented by specifying
*estyle* as *last/efirst/middle* which will alter the inter-replica
force applied to intermediate replicas by removing the contribution of
the gradient to the inter-replica force. This will only be done if a
particular intermediate replica has a lower energy than the first
replica. This should effectively prevent the intermediate replicas from
over-relaxing.
After converging a NEB calculation using an *estyle* of
*last/efirst/middle*, you should check that all intermediate replicas
@ -237,9 +236,10 @@ target energy.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

6
doc/src/fix_nonaffine_displacement.rst
View File

@ -44,7 +44,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
This fix computes different metrics of the nonaffine displacement of
particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`
@ -86,8 +86,8 @@ Both of these methods require defining a reference state. With the *fixed* refer
style, the user picks a specific timestep *nstep* at which particle positions are saved.
If peratom data is accessed from this compute prior to this timestep, it will simply be
zeroed. The *update* reference style implies the reference state will be updated every
*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
*nstep* timesteps. The *offset* reference will update the reference state *nstep*
timesteps before a multiple of *nevery* timesteps.
----------

17
doc/src/fix_property_atom.rst
View File

@ -22,6 +22,8 @@ Syntax
*mol* = molecule IDs
*q* = charge
*rmass* = per-atom mass
*temperature* = internal temperature of atom
*heatflow* = internal heat flow of atom
i_name = new integer vector referenced by name
d_name = new floating-point vector referenced by name
i2_name = new integer array referenced by name
@ -59,14 +61,18 @@ these properties for each atom in the system when a data file is read.
This fix augments the set of per-atom properties with new custom
ones. This can be useful in several scenarios.
If the atom style does not define molecule IDs, per-atom charge, or
per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
If the atom style does not define molecule IDs, per-atom charge,
per-atom mass, internal temperature, or internal heat flow, they can
be added using the *mol*\ , *q*, *rmass*, *temperature*, or *heatflow*
keywords. This could be useful to define "molecules" to use as rigid
bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
around an extra flag with atoms (stored as a molecule ID) that can be
used by various commands like :doc:`compute chunk/atom
<compute_chunk_atom>` to group atoms without having to use the group
command (which is limited to a total of 32 groups including *all*\ ).
For finite-size particles, an internal temperature and heat flow can
be used to model heat conduction as in the
:doc:`GRANULAR package <Howto_granular>`.
Another application is to use the *rmass* flag in order to have
per-atom masses instead of per-type masses. This could be used to
@ -85,9 +91,10 @@ properties that are not needed such as bond lists, which incurs some
overhead when there are no bonds.
In the future, we may add additional existing per-atom properties to
fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
"turn-on" specific properties defined by some atom styles, so they can
be easily used by atom styles that do not define them.
fix property/atom, similar to *mol*\ , *q*, *rmass*\ , *temperature*\ ,
or *heatflow* which "turn-on" specific properties defined by some atom
styles, so they can be easily used by atom styles that do not define
them.
More generally, the *i_name* and *d_name* options allow one or more
new custom per-atom vectors to be defined. Likewise the *i2_name* and

2
doc/src/fix_qeq.rst
View File

@ -232,8 +232,6 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These qeq fixes are not compatible with the GPU and USER-INTEL packages.
These qeq fixes will ignore electric field contributions from
:doc:`fix efield <fix_efield>`.

281
doc/src/fix_rigid.rst
View File

@ -171,14 +171,15 @@ Examples of large rigid bodies are a colloidal particle, or portions
of a biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those
modeled in :ref:`this paper <Zhang1>` by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consisting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the :doc:`fix shake <fix_shake>` command can also be used to rigidify small
molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
the constituent atoms as point masses.
modeled in :ref:`this paper <Zhang1>` by Sharon Glotzer's group,
clumps of granular particles, lipid molecules consisting of one or
more point dipoles connected to other spheroids or ellipsoids,
irregular particles built from line segments (2d) or triangles (3d),
and coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the :doc:`fix shake
<fix_shake>` command can also be used to rigidify small molecules of
2, 3, or 4 atoms, e.g. water molecules. That fix treats the
constituent atoms as point masses.
These fixes also update the positions and velocities of the atoms in
each rigid body via time integration, in the NVE, NVT, NPT, or NPH
@ -212,13 +213,14 @@ processors when ghost atom info is accumulated.
.. note::
To use the *rigid/small* styles the ghost atom cutoff must be
large enough to span the distance between the atom that owns the body
and every other atom in the body. This distance value is printed out
when the rigid bodies are defined. If the
:doc:`pair_style <pair_style>` cutoff plus neighbor skin does not span
this distance, then you should use the :doc:`comm_modify cutoff <comm_modify>` command with a setting epsilon larger than
the distance.
To use the *rigid/small* styles the ghost atom cutoff must be large
enough to span the distance between the atom that owns the body and
every other atom in the body. This distance value is printed out
when the rigid bodies are defined. If the :doc:`pair_style
<pair_style>` cutoff plus neighbor skin does not span this
distance, then you should use the :doc:`comm_modify cutoff
<comm_modify>` command with a setting epsilon larger than the
distance.
Which of the two variants is faster for a particular problem is hard
to predict. The best way to decide is to perform a short test run.
@ -229,49 +231,54 @@ differences may accumulate to produce divergent trajectories.
.. note::
You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix move <fix_move>`),
or you will have conflicting updates to positions and velocities
resulting in unphysical behavior in most cases. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles.
time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix
nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix move
<fix_move>`), or you will have conflicting updates to positions and
velocities resulting in unphysical behavior in most cases. When
performing a hybrid simulation with some atoms in rigid bodies, and
some not, a separate time integration fix like :doc:`fix nve
<fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the
non-rigid particles.
.. note::
These fixes are overkill if you simply want to hold a collection
of atoms stationary or have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms in
your time integration fix. E.g. use "fix 1 mobile nve" instead of
"fix 1 all nve", where "mobile" is the group of atoms that you want to
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the :doc:`velocity <velocity>` command),
setting the force on them to 0.0 (via the :doc:`fix setforce <fix_setforce>` command), and integrating them as usual
(e.g. via the :doc:`fix nve <fix_nve>` command).
These fixes are overkill if you simply want to hold a collection of
atoms stationary or have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms
in your time integration fix. E.g. use "fix 1 mobile nve" instead
of "fix 1 all nve", where "mobile" is the group of atoms that you
want to move. You can move atoms with a constant velocity by
assigning them an initial velocity (via the :doc:`velocity
<velocity>` command), setting the force on them to 0.0 (via the
:doc:`fix setforce <fix_setforce>` command), and integrating them
as usual (e.g. via the :doc:`fix nve <fix_nve>` command).
.. warning::
The aggregate properties of each rigid body are
calculated at the start of a simulation run and are maintained in
internal data structures. The properties include the position and
velocity of the center-of-mass of the body, its moments of inertia, and
its angular momentum. This is done using the properties of the
constituent atoms of the body at that point in time (or see the *infile*
keyword option). Thereafter, changing these properties of individual
atoms in the body will have no effect on a rigid body's dynamics, unless
they effect any computation of per-atom forces or torques. If the
keyword *reinit* is set to *yes* (the default), the rigid body data
structures will be recreated at the beginning of each *run* command;
if the keyword *reinit* is set to *no*, the rigid body data structures
will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you
could displace the atoms in a body or add a large velocity to each atom
in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes
of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no*
(or using the *infile* option, which implies *reinit* *no*\ ) the position
and velocity of individual atoms in the body will be reset when time
integration starts again.
The aggregate properties of each rigid body are calculated at the
start of a simulation run and are maintained in internal data
structures. The properties include the position and velocity of the
center-of-mass of the body, its moments of inertia, and its angular
momentum. This is done using the properties of the constituent
atoms of the body at that point in time (or see the *infile*
keyword option). Thereafter, changing these properties of
individual atoms in the body will have no effect on a rigid body's
dynamics, unless they effect any computation of per-atom forces or
torques. If the keyword *reinit* is set to *yes* (the default), the
rigid body data structures will be recreated at the beginning of
each *run* command; if the keyword *reinit* is set to *no*, the
rigid body data structures will be built only at the very first
*run* command and maintained for as long as the rigid fix is
defined. For example, you might think you could displace the atoms
in a body or add a large velocity to each atom in a body to make it
move in a desired direction before a second run is performed, using
the :doc:`set <set>` or :doc:`displace_atoms <displace_atoms>` or
:doc:`velocity <velocity>` commands. But these commands will not
affect the internal attributes of the body unless *reinit* is set
to *yes*\ . With *reinit* set to *no* (or using the *infile*
option, which implies *reinit* *no*\ ) the position and velocity of
individual atoms in the body will be reset when time integration
starts again.
----------
@ -316,17 +323,17 @@ to be part of rigid bodies.
.. note::
To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each atom in the
body are used to "unwrap" the atom coordinates. Thus you must ensure
that these image flags are consistent so that the unwrapping creates a
To compute the initial center-of-mass position and other properties
of each rigid body, the image flags for each atom in the body are
used to "unwrap" the atom coordinates. Thus you must ensure that
these image flags are consistent so that the unwrapping creates a
valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
:doc:`set <set>` command to specify them correctly. If a dimension is
non-periodic then the image flag of each atom must be 0 in that
dimension, else an error is generated.
particularly if the atoms in a single rigid body straddle a
periodic boundary. This means the input data file or restart file
must define the image flags for each atom consistently or that you
have used the :doc:`set <set>` command to specify them correctly.
If a dimension is non-periodic then the image flag of each atom
must be 0 in that dimension, else an error is generated.
The *force* and *torque* keywords discussed next are only allowed for
the *rigid* styles.
@ -362,12 +369,13 @@ settings from the final keyword are used.
.. note::
For computational efficiency, you may wish to turn off pairwise
and bond interactions within each rigid body, as they no longer
contribute to the motion. The :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
commands are used to do this. If the rigid bodies have strongly
overlapping atoms, you may need to turn off these interactions to
avoid numerical problems due to large equal/opposite intra-body forces
For computational efficiency, you may wish to turn off pairwise and
bond interactions within each rigid body, as they no longer
contribute to the motion. The :doc:`neigh_modify exclude
<neigh_modify>` and :doc:`delete_bonds <delete_bonds>` commands are
used to do this. If the rigid bodies have strongly overlapping
atoms, you may need to turn off these interactions to avoid
numerical problems due to large equal/opposite intra-body forces
swamping the contribution of small inter-body forces.
For computational efficiency, you should typically define one fix
@ -379,7 +387,8 @@ is more expensive.
The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheres or
ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri <atom_style>` commands for more
ellipsoids or line segments or triangles. See the :doc:`atom_style
sphere and ellipsoid and line and tri <atom_style>` commands for more
details on these kinds of particles. Finite-size particles contribute
differently to the moment of inertia of a rigid body than do point
particles. Finite-size particles can also experience torque (e.g. due
@ -389,7 +398,8 @@ orientation. These contributions are accounted for by these fixes.
Forces between particles within a body do not contribute to the
external force or torque on the body. Thus for computational
efficiency, you may wish to turn off pairwise and bond interactions
between particles within each rigid body. The :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
between particles within each rigid body. The :doc:`neigh_modify
exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
commands are used to do this. For finite-size particles this also
means the particles can be highly overlapped when creating the rigid
body.
@ -401,16 +411,17 @@ perform constant NVE time integration. They are referred to below as
the 4 NVE rigid styles. The only difference is that the *rigid* and
*rigid/small* styles use an integration technique based on Richardson
iterations. The *rigid/nve* and *rigid/small/nve* styles uses the
methods described in the paper by :ref:`Miller <Miller3>`, which are thought
to provide better energy conservation than an iterative approach.
methods described in the paper by :ref:`Miller <Miller3>`, which are
thought to provide better energy conservation than an iterative
approach.
The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT
integration using a Nose/Hoover thermostat with chains as described
originally in :ref:`(Hoover) <Hoover>` and :ref:`(Martyna) <Martyna2>`, which
thermostats both the translational and rotational degrees of freedom
of the rigid bodies. They are referred to below as the 2 NVT rigid
styles. The rigid-body algorithm used by *rigid/nvt* is described in
the paper by :ref:`Kamberaj <Kamberaj>`.
originally in :ref:`(Hoover) <Hoover>` and :ref:`(Martyna)
<Martyna2>`, which thermostats both the translational and rotational
degrees of freedom of the rigid bodies. They are referred to below as
the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt*
is described in the paper by :ref:`Kamberaj <Kamberaj>`.
The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small*
styles perform constant NPT or NPH integration using a Nose/Hoover
@ -436,12 +447,12 @@ The target pressures for each of the 6 components of the stress tensor
can be specified independently via the *x*, *y*, *z* keywords, which
correspond to the 3 simulation box dimensions. For each component,
the external pressure or tensor component at each timestep is a ramped
value during the run from *Pstart* to *Pstop*\ . If a target pressure is
specified for a component, then the corresponding box dimension will
change during a simulation. For example, if the *y* keyword is used,
the y-box length will change. A box dimension will not change if that
component is not specified, although you have the option to change
that dimension via the :doc:`fix deform <fix_deform>` command.
value during the run from *Pstart* to *Pstop*\ . If a target pressure
is specified for a component, then the corresponding box dimension
will change during a simulation. For example, if the *y* keyword is
used, the y-box length will change. A box dimension will not change
if that component is not specified, although you have the option to
change that dimension via the :doc:`fix deform <fix_deform>` command.
For all barostat keywords, the *Pdamp* parameter operates like the
*Tdamp* parameter, determining the time scale on which pressure is
@ -525,11 +536,11 @@ discussed below.
The *langevin* keyword applies a Langevin thermostat to the constant
NVE time integration performed by any of the 4 NVE rigid styles:
*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be
used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The
desired temperature at each timestep is a ramped value during the run
from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time
units and determines how rapidly the temperature is relaxed. For
*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot
be used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ .
The desired temperature at each timestep is a ramped value during the
run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (:math:`\tau` or fs or ps - see the
:doc:`units <units>` command). The random # *seed* must be a positive
@ -564,29 +575,30 @@ used. *Tchain* is the number of thermostats in the Nose Hoover chain.
This value, along with *Tdamp* can be varied to dampen undesirable
oscillations in temperature that can occur in a simulation. As a rule
of thumb, increasing the chain length should lead to smaller
oscillations. The keyword *pchain* specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom.
oscillations. The keyword *pchain* specifies the number of thermostats
in the chain thermostatting the barostat degrees of freedom.
.. note::
There are alternate ways to thermostat a system of rigid bodies.
You can use :doc:`fix langevin <fix_langevin>` to treat the individual
particles in the rigid bodies as effectively immersed in an implicit
solvent, e.g. a Brownian dynamics model. For hybrid systems with both
rigid bodies and solvent particles, you can thermostat only the
solvent particles that surround one or more rigid bodies by
appropriate choice of groups in the compute and fix commands for
temperature and thermostatting. The solvent interactions with the
rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands.
You can use :doc:`fix langevin <fix_langevin>` to treat the
individual particles in the rigid bodies as effectively immersed in
an implicit solvent, e.g. a Brownian dynamics model. For hybrid
systems with both rigid bodies and solvent particles, you can
thermostat only the solvent particles that surround one or more
rigid bodies by appropriate choice of groups in the compute and fix
commands for temperature and thermostatting. The solvent
interactions with the rigid bodies should then effectively
thermostat the rigid body temperature as well without use of the
Langevin or Nose/Hoover options associated with the fix rigid
commands.
----------
The *mol* keyword can only be used with the *rigid/small* styles. It
must be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add rigid
bodies on-the-fly during a simulation. You specify a *template-ID*
must be used when other commands, such as :doc:`fix deposit
<fix_deposit>` or :doc:`fix pour <fix_pour>`, add rigid bodies
on-the-fly during a simulation. You specify a *template-ID*
previously defined using the :doc:`molecule <molecule>` command, which
reads a file that defines the molecule. You must use the same
*template-ID* that the other fix which is adding rigid bodies uses.
@ -670,16 +682,16 @@ cross periodic boundaries during the simulation.
.. note::
If you use the *infile* or *mol* keywords and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
rfile.rigid, where "rfile" is the name of the restart file,
If you use the *infile* or *mol* keywords and write restart files
during a simulation, then each time a restart file is written, the
fix also write an auxiliary restart file with the name rfile.rigid,
where "rfile" is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an *infile* keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.
file is in the same format described above. Thus it can be used in
a new input script that restarts the run and re-specifies a rigid
fix using an *infile* keyword and the appropriate filename. Note
that the auxiliary file will contain one line for every rigid body,
even if the original file only listed a subset of the rigid bodies.
If the system has rigid bodies with finite-size overlapping particles
and the model uses the :doc:`fix gravity <fix_gravity>` command to
@ -728,10 +740,11 @@ also accounted for by this fix.
----------
If your simulation is a hybrid model with a mixture of rigid bodies and
non-rigid particles (e.g. solvent) there are several ways these rigid
fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt
<fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If your simulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with :doc:`fix nve <fix_nve>`,
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph
<fix_nh>`.
If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid
@ -741,14 +754,14 @@ particles.
If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid
bodies, and any thermostatting fix for the non-rigid particles
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`). You can also use one of the 4
NVE rigid styles for the rigid bodies and thermostat them using
:doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix
langevin <fix_langevin>` to each rigid body effectively thermostats its
translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix temp/berendsen <fix_temp_berendsen>`). You can also use one
of the 4 NVE rigid styles for the rigid bodies and thermostat them
using :doc:`fix langevin <fix_langevin>` on the group that contains
all the particles in the rigid bodies. The net force added by
:doc:`fix langevin <fix_langevin>` to each rigid body effectively
thermostats its translational center-of-mass motion. Not sure how
well it does at thermostatting its rotational motion.
If you wish to perform NPT or NPH dynamics (barostatting), you cannot
use both :doc:`fix npt <fix_nh>` and the NPT or NPH rigid styles. This
@ -774,12 +787,12 @@ to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the second and third options for a non-hybrid
simulation consisting of only rigid bodies, assuming you give :doc:`fix
npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen
<fix_press_berendsen>`) will monitor the pressure and change the box
dimensions, but not time integrate any particles. The integration of
the rigid bodies will be performed by fix rigid/nvt.
simulation consisting of only rigid bodies, assuming you give
:doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to
do. The barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix
press/berensen <fix_press_berendsen>`) will monitor the pressure and
change the box dimensions, but not time integrate any particles. The
integration of the rigid bodies will be performed by fix rigid/nvt.
----------
@ -824,10 +837,10 @@ various :doc:`output commands <Howto_output>`. The scalar value
calculated by these fixes is "intensive". The scalar is the current
temperature of the collection of rigid bodies. This is averaged over
all rigid bodies and their translational and rotational degrees of
freedom. The translational energy of a rigid body is 1/2 m v\^2, where
m = total mass of the body and v = the velocity of its center of mass.
The rotational energy of a rigid body is 1/2 I w\^2, where I = the
moment of inertia tensor of the body and w = its angular velocity.
freedom. The translational energy of a rigid body is 1/2 m v\^2,
where m = total mass of the body and v = the velocity of its center of
mass. The rotational energy of a rigid body is 1/2 I w\^2, where I =
the moment of inertia tensor of the body and w = its angular velocity.
Degrees of freedom constrained by the *force* and *torque* keywords
are removed from this calculation, but only for the *rigid* and
*rigid/nve* fixes.

3
doc/src/fix_sgcmc.rst
View File

@ -155,6 +155,9 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
This fix style requires an :doc:`atom style <atom_style>` with per atom
type masses.
At present the fix provides optimized subroutines for EAM type
potentials (see above) that calculate potential energy changes due to
*local* atom type swaps very efficiently. Other potentials are

103
doc/src/fix_ttm.rst
View File

@ -96,11 +96,11 @@ each processor, which is acceptable when the overall grid is reasonably
small. For larger grids you should use fix *ttm/grid* instead.
Fix *ttm/mod* adds options to account for external heat sources (e.g. at
a surface) and for specifying parameters that allow the electronic
heat capacity to depend strongly on electronic temperature. It is
more expensive computationally than fix *ttm* because it treats the
thermal diffusion equation as non-linear. More details on fix *ttm/mod*
are given below.
a surface) and for specifying parameters that allow the electronic heat
capacity to depend strongly on electronic temperature. It is more
expensive computationally than fix *ttm* because it treats the thermal
diffusion equation as non-linear. More details on fix *ttm/mod* are
given below.
Heat transfer between the electronic and atomic subsystems is carried
out via an inhomogeneous Langevin thermostat. Only atoms in the fix
@ -136,23 +136,23 @@ transfer between the subsystems:
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a'
where C_e is the specific heat, rho_e is the density, kappa_e is the
thermal conductivity, T is temperature, the "e" and "a" subscripts
represent electronic and atomic subsystems respectively, g_p is the
coupling constant for the electron-ion interaction, and g_s is the
electron stopping coupling parameter. C_e, rho_e, and kappa_e are
specified as parameters to the fix. The other quantities are derived.
The form of the heat diffusion equation used here is almost the same
as that in equation 6 of :ref:`(Duffy) <Duffy>`, with the exception that the
electronic density is explicitly represented, rather than being part
of the specific heat parameter.
where :math:`C_e` is the specific heat, :math:`\rho_e` is the density,
:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the
"e" and "a" subscripts represent electronic and atomic subsystems
respectively, :math:`g_p` is the coupling constant for the electron-ion
interaction, and :math:`g_s` is the electron stopping coupling
parameter. :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are
specified as parameters to the fix *ttm* or *ttm/grid*. The other
quantities are derived. The form of the heat diffusion equation used
here is almost the same as that in equation 6 of :ref:`(Duffy) <Duffy>`,
with the exception that the electronic density is explicitly
represented, rather than being part of the specific heat parameter.
Currently, the TTM fixes assume that none of the user-supplied
parameters will vary with temperature. Note that :ref:`(Duffy)
<Duffy>` used a tanh() functional form for the temperature dependence
of the electronic specific heat, but ignored temperature dependencies
of any of the other parameters. See more discussion below for fix
ttm/mod.
parameters will vary with temperature. Note that :ref:`(Duffy) <Duffy>`
used a tanh() functional form for the temperature dependence of the
electronic specific heat, but ignored temperature dependencies of any of
the other parameters. See more discussion below for fix *ttm/mod*.
.. note::
@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations):
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
where theta is the Heaviside step function, I_0 is the (absorbed)
laser pulse intensity for ablation simulations, l_skin is the depth
of skin-layer, and all other designations have the same meaning as in
the former equation. The duration of the pulse is set by the parameter
*tau* in the *init_file*.
where :math:`\theta` is the Heaviside step function, :math:`I_0` is the
(absorbed) laser pulse intensity for ablation simulations,
:math:`l_{skin}` is the depth of the skin-layer, and all other
designations have the same meaning as in the former equation. The
duration of the pulse is set by the parameter *tau* in the *init_file*.
Fix ttm/mod also allows users to specify the dependencies of C_e and
kappa_e on the electronic temperature. The specific heat is expressed
as
Fix *ttm/mod* also allows users to specify the dependencies of
:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The
specific heat is expressed as
.. math::
C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
where *X* = T_e/1000, and the thermal conductivity is defined as
kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion
coefficient.
where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is
defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where
:math:`D_e` is the thermal diffusion coefficient.
Electronic pressure effects are included in the TTM model to account
for the blast force acting on ions because of electronic pressure
gradient (see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
Electronic pressure effects are included in the TTM model to account for
the blast force acting on ions because of electronic pressure gradient
(see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
acting on an ion is:
.. math::
@ -293,25 +293,26 @@ acting on an ion is:
{\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec
F}_{langevin} - \nabla P_e/n_{ion}
where F_langevin is a force from Langevin thermostat simulating
electron-phonon coupling, and nabla P_e/n_ion is the electron blast
force.
where :math:`F_{langevin}` is a force from Langevin thermostat
simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is
the electron blast force.
The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e
The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot
C_e \cdot T_e`
The current fix ttm/mod implementation allows TTM simulations with a
The current fix *ttm/mod* implementation allows TTM simulations with a
vacuum. The vacuum region is defined as the grid cells with zero
electronic temperature. The numerical scheme does not allow energy
exchange with such cells. Since the material can expand to previously
unoccupied region in some simulations, the vacuum border can be
allowed to move. It is controlled by the *surface_movement* parameter
in the *init_file*. If it is set to 1, then "vacuum" cells can be
changed to "electron-filled" cells with the temperature *T_e_min* if
atoms move into them (currently only implemented for the case of
1-dimensional motion of flat surface normal to the X axis). The
initial borders of vacuum can be set in the *init_file* via *lsurface*
and *rsurface* parameters. In this case, electronic pressure gradient
is calculated as
unoccupied region in some simulations, the vacuum border can be allowed
to move. It is controlled by the *surface_movement* parameter in the
*init_file*. If it is set to 1, then "vacuum" cells can be changed to
"electron-filled" cells with the temperature *T_e_min* if atoms move
into them (currently only implemented for the case of 1-dimensional
motion of a flat surface normal to the X axis). The initial locations of
the interfaces of the electron density to the vacuum can be set in the
*init_file* via *lsurface* and *rsurface* parameters. In this case,
electronic pressure gradient is calculated as
.. math::
@ -319,10 +320,10 @@ is calculated as
\frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta
x}-(C_e{}T_e)_{x}}{\Delta x} \right]
where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
:ref:`(Pisarev) <Pisarev>`)
where :math:`\lambda` is the electron mean free path (see :ref:`(Norman)
<Norman>`, :ref:`(Pisarev) <Pisarev>`)
The fix ttm/mod parameter file *init_file* has the following syntax.
The fix *ttm/mod* parameter file *init_file* has the following syntax.
Every line with an odd number is considered as a comment and
ignored. The lines with the even numbers are treated as follows:

175
doc/src/fix_wall_flow.rst Normal file
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@ -0,0 +1,175 @@
.. index:: fix wall/flow
.. index:: fix wall/flow/kk
fix wall/flow command
=====================
Accelerator Variants: *wall/flow/kk*
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID wall/flow axis vflow T seed N coords ... keyword value
* ID, group-ID are documented in :doc:`fix <fix>` command
* wall/flow = style name of this fix command
* axis = flow axis (*x*, *y*, or *z*)
* vflow = generated flow velocity in *axis* direction (velocity units)
* T = flow temperature (temperature units)
* seed = random seed for stochasticity (positive integer)
* N = number of walls
* coords = list of N wall positions along the *axis* direction in ascending order (distance units)
* zero or more keyword/value pairs may be appended
* keyword = *units*
.. parsed-literal::
*units* value = *lattice* or *box*
*lattice* = wall positions are defined in lattice units
*box* = the wall positions are defined in simulation box units
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all wall/flow x 0.4 1.5 593894 4 2.0 4.0 6.0 8.0
Description
"""""""""""
.. versionadded:: 17Apr2024
This fix implements flow boundary conditions (FBC) introduced in
:ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
The goal is to generate a stationary flow with a shifted Maxwell
velocity distribution:
.. math::
f_a(v_a) \propto \exp{\left(-\frac{m (v_a-v_{\text{flow}})^2}{2 kB T}\right)}
where :math:`v_a` is the component of velocity along the specified
*axis* argument (a = x,y,z), :math:`v_{\text{flow}}` is the flow
velocity specified as the *vflow* argument, *T* is the specified flow
temperature, *m* is the particle mass, and *kB* is the Boltzmann
constant.
This is achieved by defining a series of *N* transparent walls along
the flow *axis* direction. Each wall is at the specified position
listed in the *coords* argument. Note that an additional transparent
wall is defined by the code at the boundary of the (periodic)
simulation domain in the *axis* direction. So there are effectively
N+1 walls.
Each time a particle in the specified group passes through one of the
transparent walls, its velocity is re-assigned. Particles not in the
group do not interact with the wall. This can be used, for example, to
add obstacles composed of atoms, or to simulate a solution of complex
molecules in a one-atom liquid (note that the fix has been tested for
one-atom systems only).
Conceptually, the velocity re-assignment represents creation of a new
particle within the system with simultaneous removal of the particle
which passed through the wall. The velocity components in directions
parallel to the wall are re-assigned according to the standard Maxwell
velocity distribution for the specified temperature *T*. The velocity
component perpendicular to the wall is re-assigned according to the
shifted Maxwell distribution defined above:
.. math::
f_{\text{a generated}}(v_a) \propto v_a f_a(v_a)
It can be shown that for an ideal-gas scenario this procedure makes
the velocity distribution of particles between walls exactly as
desired.
Since in most cases simulated systems are not an ideal gas, multiple
walls can be defined, since a single wall may not be sufficient for
maintaining a stationary flow without "congestion" which can manifest
itself as regions in the flow with increased particle density located
upstream from static obstacles.
For the same reason, the actual temperature and velocity of the
generated flow may differ from what is requested. The degree of
discrepancy is determined by how different from an ideal gas the
simulated system is. Therefore, a calibration procedure may be
required for such a system as described in :ref:`(Pavlov)
<fbc-Pavlov2>`.
Note that the interactions between particles on different sides of a
transparent wall are not disabled or neglected. Likewise particle
positions are not altered by the velocity reassignment. This removes
the need to modify the force field to work correctly in cases when a
particle is close to a wall.
For example, if particle positions were uniformly redistributed across
the surface of a wall, two particles could end up too close to each
other, potentially causing the simulation to explode. However due to
this compromise, some collective phenomena such as regions with
increased/decreased density or collective movements are not fully
removed when particles cross a wall. This unwanted consequence can
also be potentially mitigated by using more multiple walls.
.. note::
When the specified flow has a high velocity, a lost atoms error can
occur (see :doc:`error messages <Errors_messages>`). If this
happens, you should ensure the checks for neighbor list rebuilds,
set via the :doc:`neigh_modify <neigh_modify>` command, are as
conservative as possible (every timestep if needed). Those are the
default settings.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to
this fix.
No global or per-atom quantities are stored by this fix for access by
various :doc:`output commands <Howto_output>`.
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 :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
Fix *wall_flow* is part of the EXTRA-FIX package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Flow boundary conditions should not be used with rigid bodies such as
those defined by a "fix rigid" command.
This fix can only be used with periodic boundary conditions along the
flow axis. The size of the box in this direction must not change. Also,
the fix is designed to work only in an orthogonal simulation box.
Related commands
""""""""""""""""
:doc:`fix wall/reflect <fix_wall>` command
Default
"""""""
The default for the units keyword is lattice.
----------
.. _fbc-Pavlov1:
**(Pavlov1)** Pavlov, Kolotinskii, Stegailov, "GPU-Based Molecular Dynamics of Turbulent Liquid Flows with OpenMM", Proceedings of PPAM-2022, LNCS (Springer), vol. 13826, pp. 346-358 (2023)
.. _fbc-Pavlov2:
**(Pavlov2)** Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)

7
doc/src/fix_widom.rst
View File

@ -195,8 +195,11 @@ doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is **required**.
Can be run in parallel, but aspects of the GCMC part will not scale well
in parallel. Only usable for 3D simulations.
This fix style requires an :doc:`atom style <atom_style>` with per atom
type masses.
Can be run in parallel, but some aspects of the insertion procedure
will not scale well in parallel. Only usable for 3D simulations.
Related commands

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